We've talked about this - #1093 maybe we can start there.

Jegelewicz on 16 Jul 2019

We've already gone through the "student" discussion in
https://github.com/ArctosDB/arctos/issues/1093. Let's not go there again.
Reviving another related request from the earlier thread:
4) Dusty, please get rid of "ID of kin" as default nature of ID; leave
blank value and require selection from list.
… https://github.com/ArctosDB/arctos/issues/1093#

On Tue, Jul 16, 2019 at 3:34 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

We've talked about this - #1093
https://github.com/ArctosDB/arctos/issues/1093 maybe we can start there.

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campmlc on 16 Jul 2019

I agree strongly that we should remove ID of Kin as the default value - too
many errors result. Leave it blank & require it be filled.

student vs expert vs curatorial - I sometimes have a hard time deciding
between my own IDs - are they expert or student? The addition of curatorial
as an option makes this decision making even worse. Do I use expert or
curatorial (or student)? I've argued before and will again that the least
ambiguous set of choices for this would be 'expert' vs 'non-expert'.
Non-expert is the clear choice for any IDs not made by an expert and*
knowing whether it was made by an expert or not is the most important thing
to know about an id*. If someone told me these IDs were made by students
and these others by curatorial staff I would wonder about my own curatorial
staff, who are often students... and myself.. and I consider myself a
student of many taxa but an expert in just a few. Also, I'm an expert at
getting ALL insects ID'd to order, but only an expert at getting some
insects ID'd to species.

So I argue for replacing both 'student' and 'curatorial' with 'non-expert'

I agree that 'field' is ambiguous - if an expert is in the field and is
confident of what the ID is without recourse to keys then use 'expert'
instead. If it's not an expert, use 'non-expert'. Add remarks to the
remarks if desired.

I've never used 'ID to species group' and agree with Dusty that we have
better ways to show that - plus we still would want to know if it was an
expert who made that ID to species group and this option prevents us from
storing that information.

Geographic distribution - climate change is making some geographic regions
more tolerable than they had been previously.... perhaps this should be
restricted to remarks. Eg. an expert who decides what it is and then adds
this information to the remarks is a more valuable ID than just using
'geographic distribution' as if anyone (non expert vs expert) could safely
make an identification of the same reliability.

I think photograph should be in remarks also - an expert ID based on a
photo is a lot different than a non-expert ID based on a photo.

published referral- oftentimes we don't know who did the IDs of the species
listed in papers (sadly) and it's not safe to assume it was one or more of
the authors. This is similar to legacy but makes it clear the ID came from
a publication, not a label on a specimen in front of you.

revised taxonomy - this is important to record but I dislike that it hides
information about expert vs non-expert ID... for example, if I loan
specimens to an expert and get them back and later one of the species is
moved to a new genus I update all the records with the new name and myself
as the determiner and use revised taxonomy. But when these data are shared
to aggregators or downloaded by users, they rarely or don't see that the
specimens were ID'd by an expert... they only see the most recent ID by
myself, a non-expert, who didn't even look at the specimens, I just updated
the name.

I've long wished this could be altered somehow - perhaps needing new fields
to store information about this while retaining the ID of the last person
who actually looked at the specimens... somehow.

my 2 cents.

-Derek

On Tue, Jul 16, 2019 at 1:48 PM Mariel Campbell notifications@github.com
wrote:

We've already gone through the "student" discussion in
https://github.com/ArctosDB/arctos/issues/1093. Let's not go there again.
Reviving another related request from the earlier thread:
4) Dusty, please get rid of "ID of kin" as default nature of ID; leave
blank value and require selection from list.
… https://github.com/ArctosDB/arctos/issues/1093#

On Tue, Jul 16, 2019 at 3:34 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

We've talked about this - #1093
https://github.com/ArctosDB/arctos/issues/1093 maybe we can start
there.

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[email protected]

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DerekSikes on 17 Jul 2019

I'll say what I said before:

I don't believe that we are qualified to make an assessment of the expertise of any identifier. Wouldn't it be better to only provide objective data? Most of the options are pretty much that.

Most of these designations are opinions as Derek demonstrated with his "I am an expert, I am a student" argument. The rest would be supported with a remark or citation. If the ID was made in a publication (revised taxonomy), then there should be a citation - no need to say any more. I feel like this field is unnecessary in a way and I don't see an equivalent DWC Identification term.

Jegelewicz on 17 Jul 2019

for example, if I loan
specimens to an expert and get them back and later one of the species is
moved to a new genus I update all the records with the new name and myself
as the determiner and use revised taxonomy. But when these data are shared
to aggregators or downloaded by users, they rarely or don't see that the
specimens were ID'd by an expert... they only see the most recent ID by
myself, a non-expert, who didn't even look at the specimens, I just updated
the name.

I've long wished this could be altered somehow - perhaps needing new fields
to store information about this while retaining the ID of the last person
who actually looked at the specimens... somehow.

This is an aggregator issue. Anyone looking at the record in Arctos could see what happened. Until GBIF&Co can handle the multiple IDs, I'm not sure we can do anything to make things look better on their end. I suggest you open an issue with iDigBio about it and start a wider discussion.

Jegelewicz on 17 Jul 2019

I knew this was eerily familiar...

Looks like we're more or less agreed on 'legacy'-->'unknown' - I'll make that change if nobody stops me soonish.

remove ID of Kin

That sort of thing gets lost in these kind of Issues. I moved it to https://github.com/ArctosDB/arctos/issues/1868, which I think I'm just going to have to do in production, which is probably going to be disruptive. I re-prioritized and will try to sneak it in ASAP.

I don't believe that we are qualified to make an assessment of the expertise of any identifier. Wouldn't it be better to only provide objective data?

YES!

I don't think we're going to convince anyone that a dedicated volunteer necessarily produces lower-quality IDs than random 'students,' or that becoming a grad student magically makes someone an "expert" for everything, everywhere, using any technique (and I can't see any other way to interpret some of the data in Arctos).

Conversely, about anyone could do a bang-up job of feeding a sequence to genbank and recording whatever flops out.

Geographic distribution - climate change

Excellent point.

as if anyone (non expert vs expert) could safely make an identification of the same reliability.

That's my reading of the current documentation - "looks like a woodpecker - we're HERE - must be THAT woodpecker...."

I consider myself a student of many taxa but an expert in just a few.

That I think is getting close to useful, but I also suspect others working with those taxa know that and don't need to be told. That is, technique+agent gets at "expertness" (or the lack thereof), and we don't need an explicit pigeonhole.

There's also some weird "experience factor" in there. The first ID you make with some new technique/taxa/whatever probably isn't as good as your 10,000th. I have no idea what to do with that....

non-expert

That makes sense only if we're contrasting it with "expert," and I obviously see dubious value in "expert."

argue for replacing both 'student' and 'curatorial' with 'non-expert'

I'm not crazy about the vocabulary, but completely agree with the direction.

published referral

Fair enough, and I suppose that more or less reflects the structure of citations. Minimally they didn't reject the possibility that the thing is whatever they called it.

I think that's another reason to hate "expert" (or ranking identifiers in general) as well - I'd guess a fair number of these get entered as "expert" (they're publishing on the taxa, after all), if we're using the terms arbitrarily then they can't really DO STUFF. Maybe that's just a matter of documentation.

revised taxonomy

Interesting point. I might be tempted to bring the agent and technique (if we had such a thing...) over from the previous ID, which would preserve that, but there may be some unjustified assumptions in that too - eg, maybe the 'expert' DOES NOT think "Myodes" is just another way of spelling "Clethrionomys" and your curatorial assumptions about the relationship between those names add or subtract something from the original. That would also remove the fact that the revision is your assumption. You may be right in that we're missing something, but I can't quite see what.

dustymc on 17 Jul 2019

I have not read this whole thread in detail, but I think we are confounding who is making the ID (expert, student, etc.) with the basis for the ID.

Can we make this more about the basis for the Identification:

Geographic: Identification based on range maps or textual descriptions of geographic distribution. [We use this all the time for subspecies of birds and mammals, so have to keep it]
Molecular: Identification based on comparative genetic data.
Phenotype: Identification based on qualitative or quantitative examination of external characters. [field would apply here]
ID of kin: as above.

etc. (I'd need to think about this for every existing value, and there may be new ways we're not thinking about).

The 'who' part (expert or non-expert) should be through the agent making the determination. e.g., agent Peter Pyle (=expert) made identification based on phenotype on a specific date.

ccicero on 17 Jul 2019

👍1

Thanks Carla - I like this direction, I just didn't know anyone else did!

From your comments, here's a first pass at mapping. If we go here we could probably do better for many of the unknowns - eg, IDs by {person} or before {date} or ... could get "upgraded" to something more specific.

ID of kin, geographic distribution, and revised taxonomy are "dependent" or secondary IDs; you need to see the mother's ID to know anything about how much you should trust the embryo's, a taxonomic revision is basically just a search term and the important data is in a previous identification, and geographic distribution is (from my perspective) pretty close to useless by itself, but I can definitely see how it adds value as a 'suggestion' on top of that 'Peter Pyle (=expert) made identification based on phenotype on a specific date' "primary" ID.

I'm still not crazy about the idea of identifications whose validity hinges on the accuracy of locality data.

I'm not sure how to model that (something about "accepted" getting more complex, probably) and I'm certainly not sure how to ship it to GBIF, but it feels like there's some _correct_ in there somewhere....

Some sort of 'accepted, but not all you need to know' "acceptedness" might also take care of the "these 12 techniques all say _Bla blah_" that might otherwise get lumped into "published referral."

dustymc on 17 Jul 2019

Seems the tide is shifting against my interest in maintaining 'expert' as
an option. After some thought I realized I've only used that field for a
search on 'expert' once.

I wanted to see how many Identifications I had made as an 'expert' vs how
many I had made as a 'student'. I used this information in my promotion and
tenure file. There were lots in both categories but the ones as expert were
of course more valuable. It would be a terrible loss of information to not
be able to distinguish between these two types of identifications. I would
be unable to perform this search just using taxa I know well (and it would
take separate searches on all the different taxa....) because there are too
many to remember and it depends on how well written were the keys I was
using etc. I'm a beetle specialist but for some beetle groups I can't
perform expert IDs while for others I can. When I enter the information on
the ID into Arctos I assess my confidence in the ID at that point. It's
valuable data.

These terms are vague yes, but they are an attempt at categorizing
confidence in the reliability of the ID. ( I wouldn't want to have to rank
our confidence in an ID on a 10 point scale, that would be horrible).
Perhaps we need a new field for this, since it is different information
than HOW the ID was made.

Perhaps we need a field named "ID confidence" and all those marked with
method = expert now should get "ID confidence = high" and all those marked
with method = student (or curatorial) should get "ID confidence = not high"
.

Also, since we have the method of 'molecular' it's safe to assume that all
IDs that were made by 'expert' or 'student' could be replaced by
'phenotype' rather than 'unknown'. If someone wasn't using phenotype they'd
have specified what they were using. Phenotype is the default.

-Derek

On Tue, Jul 16, 2019 at 9:34 PM dustymc notifications@github.com wrote:

Thanks Carla - I like this direction, I just didn't know anyone else did!

From your comments, here's a first pass at mapping. If we go here we could
probably do better for many of the unknowns - eg, IDs by {person} or before
{date} or ... could get "upgraded" to something more specific.
old new Hu?
ID of kin ID of kin secondary; see below
ID to species group unknown
curatorial unknown
erroneous citation unknown This belongs in
https://arctos.database.museum/info/ctDocumentation.cfm?table=CTCITATION_TYPE_STATUS,
not sure what it's doing here too??
expert unknown
field phenotype
geographic distribution geographic distribution secondary; see below
legacy unknown
molecular data genotype I don't really care what the terminology is, but
we should strive for consistency if possible. (Maybe nongenetic molecules
are used in IDs??)
photograph phenotype
published referral published referral?? Ideally these would come from the
nature of the publication, but that could require multiple values. I
suppose as long as the list is short "phenotype; genotype" isn't THAT evil
revised taxonomy revised taxonomy secondary; see below
student unknown Maybe these are all "phenotype"??

ID of kin, geographic distribution, and revised taxonomy are "dependent"
or secondary IDs; you need to see the mother's ID to know anything about
how much you should trust the embryo's, a taxonomic revision is basically
just a search term and the important data is in a previous identification,
and geographic distribution is (from my perspective) pretty close to
useless by itself, but I can definitely see how it adds value as a
'suggestion' on top of that 'Peter Pyle (=expert) made identification based
on phenotype on a specific date' "primary" ID.

I'm still not crazy about the idea of identifications whose validity
hinges on the accuracy of locality data.

I'm not sure how to model that (something about "accepted" getting more
complex, probably) and I'm certainly not sure how to ship it to GBIF, but
it feels like there's some correct in there somewhere....

Some sort of 'accepted, but not all you need to know' "acceptedness" might
also take care of the "these 12 techniques all say Bla blah" that might
otherwise get lumped into "published referral."

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
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http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
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DerekSikes on 17 Jul 2019

@DerekSikes I don't think I see a big-picture problem with that.

this specimen was identified using phenotype
the person doing the ID, at the time they were doing the ID, had {"experience factor"/confidence/whatever}

I just don't like confounding those concepts in one field. If I'm a geneticist looking for cryptic species, I probably only want things IDed using some sort of decent non-genetic technique, and our current data don't consistently support that. The ability to add "[not]confidently IDed" to that just seems like a bonus.

(I also don't much trust those data, but maybe that's another issue.)

And on that note, it probably takes us back to some sort of vocabulary/definition nightmare, but I do think there's some distinction somewhere between "phenotype, as in microscopes and slides and trait matrices and such" and "phenotype, as in it just looked like a badger." Maybe we do need to retain (and better define) "field" or something like it.

I'm not sure I understand this:

wouldn't want to have to rank our confidence in an ID on a 10 point scale, that would be horrible

anything using expert/student (and synonyms) is basically ranking confidence on a 2-point scale, no? I'm not sure how many points are in between "I just bought a field guide in the gift shop" and "I am describing the holotype" but it does seem like some sort of confidence scale.

No problem to adjust the migration path - I'll be asking lots of questions if we get to that point.

dustymc on 17 Jul 2019

@DerekSikes why does it matter if you were an expert or a student - effort was involved either way. Is every ID I made less valuable because it was a student ID? It may have been an excellent addition to my knowledge base to make those IDs and some ID is better than "Animalia", correct? Never mind that you were the one deciding whether you were an expert or student? That seems like you could rig your own promotion...not that I'm accusing you of that, but just trying to make the point that "expert" and "non-expert" are subjective and one person's expert will be another person's non-expert. These kinds of criteria seem a poor way to determine a promotion and I am not in favor of Arctos becoming the arbiter of people's employment path.

Jegelewicz on 17 Jul 2019

I'm not sure I understand this:

wouldn't want to have to rank our confidence in an ID on a 10 point

scale, that would be horrible

anything using expert/student (and synonyms) is basically ranking
confidence on a 2-point scale, no?

Yes, a 2- point scale is reasonable. Even deciding how to rank these on a
3-point scale would be hard and hardly reproducible, even for the same
person at different times of the day! a 10 point scale would be nuts.

-Derek

On Wed, Jul 17, 2019 at 7:32 AM dustymc notifications@github.com wrote:

@DerekSikes https://github.com/DerekSikes I don't think I see a
big-picture problem with that.

this specimen was identified using phenotype

the person doing the ID, at the time they were doing the ID, had
{"experience factor"/confidence/whatever}

I just don't like confounding those concepts in one field. If I'm a
geneticist looking for cryptic species, I probably only want things IDed
using some sort of decent non-genetic technique, and our current data don't
consistently support that. The ability to add "[not]confidently IDed" to
that just seems like a bonus.

(I also don't much trust those data, but maybe that's another issue.)

And on that note, it probably takes us back to some sort of
vocabulary/definition nightmare, but I do think there's some distinction
somewhere between "phenotype, as in microscopes and slides and trait
matrices and such" and "phenotype, as in it just looked like a badger."
Maybe we do need to retain (and better define) "field" or something like it.

I'm not sure I understand this:

wouldn't want to have to rank our confidence in an ID on a 10 point scale,
that would be horrible

anything using expert/student (and synonyms) is basically ranking
confidence on a 2-point scale, no? I'm not sure how many points are in
between "I just bought a field guide in the gift shop" and "I am describing
the holotype" but it does seem like some sort of confidence scale.

No problem to adjust the migration path - I'll be asking lots of questions
if we get to that point.

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University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

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http://www.uaf.edu/museum/collections/ento/
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DerekSikes on 17 Jul 2019

I think we're also drastically under-using id_sensu (fkey-->publication); it could clarify some of the ambiguity in "expertness" (or serve as an independent measure of "expertness") for anyone who wants to dig, along with the usual purpose of clarifying the taxon concept.

I was looking at phenotype, I think I'm really good at this, my reference is https://isbnsearch.org/isbn/9781426327407
I was looking at phenotype, I think I'm really good at this, my reference is https://isbnsearch.org/isbn/9780394507637
I was looking at phenotype, I think I'm really good at this, my reference is https://dx.doi.org/10.3897%2Fzookeys.789.24261

dustymc on 17 Jul 2019

👍1

Man, you're good at a lot of stuff!! :-)

Jegelewicz on 17 Jul 2019

Don't distract me, I'm still countin' legs.

dustymc on 17 Jul 2019

😄1

BTW, I retract my comment about DWC - it seems like we are trying to fill identificationVerificationStatus with this. This standard is defined as : Comments or notes about the Identification. Pretty sure no one is going to know what most of our current terms mean and also pretty sure most people will know what the terms in Carla's list do!

2160

Jegelewicz on 17 Jul 2019

I underuse that because to use it properly I'd have to have all the keys I
use already loaded into Arctos publications to link to & this would be a
massive data entry project unto itself.

Love the idea, but it fails due to cost of getting content in to make the
idea work.

-D

On Wed, Jul 17, 2019 at 8:48 AM dustymc notifications@github.com wrote:

I think we're also drastically under-using id_sensu (fkey-->publication);
it could clarify some of the ambiguity in "expertness" (or serve as an
independent measure of "expertness") for anyone who wants to dig, along
with the usual purpose of clarifying the taxon concept.

I was looking at phenotype, I think I'm really good at this, my
reference is https://isbnsearch.org/isbn/9781426327407

I was looking at phenotype, I think I'm really good at this, my
reference is https://isbnsearch.org/isbn/9780394507637

I was looking at phenotype, I think I'm really good at this, my
reference is https://dx.doi.org/10.3897%2Fzookeys.789.24261

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+++++++++++++++++++++++++++++++++++
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
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DerekSikes on 18 Jul 2019

to use it properly I'd have to have all the keys I use already loaded into Arctos publications to link to & this would be a massive data entry project unto itself.

Maybe we can automate this a bit? See #2176

Jegelewicz on 18 Jul 2019

I reiterate that I think we can/should get to the 'expert' vs 'student' etc issue via agents. ID is made by a certain person on a certain date. The person could be a student at one point in time, a post-doc (more of an expert) at another time, and a curator (=expert) at a third time. Also, I would say that undergraduate student and graduate student have different levels of expertise, and that doesn't come in the 'student' value for ID.

We should separate the how from the who. This would involve expanding on agents and adding agent role over time to create history (now role is just in remarks or maybe address):
agent X1 = graduate student between dates A and B
agent X2 = postdoc between dates C and D
agent X3= curator between dates E and F

then apply one of those three agent values to the determination.

???

ccicero on 18 Jul 2019

👍1

I would say that undergraduate student and graduate student have different levels of expertise

Still a matter of opinion and varies by the student involved. I really dislike adding our opinions. Facts are good - the position of the agent at the time of ID seems like fair information to pass along. Users can decide what that means (my grad student may be more of an "expert" than someone else's tenured faculty depending on the organism involved....).

Jegelewicz on 18 Jul 2019

If someone does something that does not suck with publications (or taxonomy, or agents, or...) it should be trivial to plug in, in any capacity from making something trivial better to just replacing our model. Not holding my breath...

If the publications have DOIs, it should be fairly easy to sprinkle the create form around. (I doubt these do??) If the authors submit ORCID with the publication and to Arctos I could magic the author part, which is about 90% of the current work in creating a publication. (Even less likely, I'm sure.)

Unrelatedish, if one publication here is too much work then maintaining a taxon concepts model does not seem remotely realistic. This is not the first time that idea has surfaced, or at least caused some ripples.

The intent of "student" has always been 'one willing to learn,' and the documentation has always supported that.

@ccicero I don't think this is something that can be normalized to people. If I bring you a North American bird, I'm pretty much just going to believe whatever you tell me. If I bring you a deepwater coral larvae - well, maybe not so much. (Nevermind, I think I figured it out below...)

I think the really critical thing here is separating technique. That's going to open up a whole new world of ways to query the data, let people get at really fundamental things - do genetics and morphology support the same hypotheses? - that just aren't accessible in our data currently.

If there's some value in ranking the confidence of the ID, I can't see how it detracts from anything. I don't think I'd ever use or believe it, but I also don't think it'd ever prevent me from doing anything so I'm fine with it.

Actually I might use and believe it.

And on that note, it probably takes us back to some sort of vocabulary/definition nightmare, but I do think there's some distinction somewhere between "phenotype, as in microscopes and slides and trait matrices and such" and "phenotype, as in it just looked like a badger." Maybe we do need to retain (and better define) "field" or something like it.

The "confidence score" could be a useful way to get at that - "Hi I'm me and despite whatever my agent-stuff might imply, you shouldn't trust me very much on this particular ID."

https://github.com/ArctosDB/arctos/issues/1873 might be the best way to organize your data - it would require a few more relationships ("graduate student of" etc.). Certainly nothing above prevents those agent-data-including queries. And including the taxa used in the IDs brings the agent's 'expertness' into perspective....and AHA!, maybe, I think.

So Carla+undergrad+Pipilo finds birds IDed between certain dates (defined in agent-data) by a certain agent - essentially a dynamic "trust factor."

So Carla+postdoc+Pipilo [+phenology + whatever else is relevant] finds birds a different set of birds (unless there are re-ids) under a different "trust factor" (still dynamically defined by the user at that moment).

So if we add one more field ("confidence score"?? Need a name) and a categorical code table (with 2 categories to start with) to feed it, I think everybody's happy and this is just a matter of vocabulary and eventually UI to hook deeper into agents.

Yay us?!?

dustymc on 18 Jul 2019

I think we are converging on something. I agree @Jegelewicz about sticking to facts. By adding a role explicitly to agents (undergraduate student, graduate student, postdoc, curator, etc.), it gets at the status of a person during a certain tenure without saying anything about confidence in that person.

I'm not sure I like 'confidence score' - that seems pretty subjective. Leave that to the person using the data. Cicero+Pipilo+audio (audio, video should be other categories of 'how') would have fairly high confidence, but the person using the data could/should interpret based on knowing something about my research rather than us providing that info.

--> I think the really critical thing here is separating technique. That's going to open up a whole new world of ways to query the data, let people get at really fundamental things - do genetics and morphology support the same hypotheses? - that just aren't accessible in our data currently.

This is what I'm getting at. We should work on coming up with a vocabulary for technique, and that should be separate from information about the person and his/her role/status/capacity. We'd need to be able to apply >1 technique to an ID.

DNA sequence
genomics
morphology
coloration
microscopy
audio
video
etc.

ccicero on 18 Jul 2019

👍1

By adding a role explicitly to agents

Minor point: adding a role to RELATIONSHIPS (which are already scheduled to get a date-component). That'll also let me get at WHERE you're a student-or-whatever, so I can add a little extra statistical weight to graduates of Dusty's Institoot o hi-er learnin'...

'confidence score' - that seems pretty subjective.

Yes, I believe that's the point.

(audio, video should be other categories of 'how'

I'm not quite sure that's correct - it's more "behavior" or perhaps "song" - like 'photo' it's the information, not the media, that we care about - but yes, I noticed that gap as well.

So "Cicero+Pipilo+audio" is the "baseline possible."

You can ignore the 'confidence score' (when searching and creating IDs) for most stuff.

If you're trying to ID a bird off of a damaged tape and you just can't quite hear enough to be sure or something, you can use 'confidence score' as a searchable way to flag that particular ID. (And I can use your agent info to not only get at how much I trust your IDs, but also how much I trust your evaluation of your IDs!)

Minimally, I don't think it can detract from anything else, and it seems that some of us have a use case for it. Ideally, perhaps it does add some real less-subjective value in some specific situations.

We'd need to be able to apply >1 technique to an ID.

That's probably a simpler approach than my vague ideas regarding "secondary" or "dependent" IDs. (And the "cool toys" comment in https://github.com/ArctosDB/internal/issues/27#issuecomment-512071298 might make it trivial without mucking with the structure - not 100% sure of that.)

Would this be one term/list, or perhaps a general+specific split - eg,

morphology; coloration; microscopy

or

general: morphology
specific: coloration; microscopy

??

dustymc on 18 Jul 2019

I'm very much in favor of a field for 'confidence score.'

In entomology we make a big deal about identifications. I try to train my
students to work within their skill set - don't try to ID something to
species until you've shown that you can reliably ID at higher levels first
(orders & families).

A 2-category confidence score gives one a way of saying "high confidence =
my reputation is on the line, if I got this wrong I'd be embarrassed and
suffer reputational damage. Thus I will use this only when I'm really
confident."

"not-high confidence = I did my best but I'm not an expert on this group
and if I got it wrong at least I warned you I wasn't that confident in the
ID. No reputational damage suffered."

Granted, for older collections where most of the databasing is being done
of specimens ID'd in the past & not by the curators/CM staff themselves,
this is harder to use if you don't know the people and their reputations
for expertise with certain taxa. However, in UAM entomology we make 40+
loans a year of tens of thousands of specimens and we loan them to people
doing taxonomic work on the groups who know these taxa better or as well as
anyone else alive. When these specimens come back from loan I mark their
IDs as 'expert' - this is useful because in 100 years folks might have a
hard time working out who was an expert on which taxa when... etc.

So I'm in favor of 'confidence score' with 2 categories. Deciding on the
names for these 2 categories is tricky though. I like 'expert' and
'non-expert' which is more obvious and means different things than 'high'
vs 'not-high' because people would interpret 'not-high' as synonymous with
'low-confidence' even though that's not a safe assumption, it'll still
happen. Or we could use numbers 1 vs 0 (but I prefer 'expert' and
'non-expert'

Also, I reiterate that all IDs by experts and students would be method =
phenotype since that's the default method, if molecular or other methods
had been used, they'd have been specified.

-Derek

On Thu, Jul 18, 2019 at 8:08 AM dustymc notifications@github.com wrote:

By adding a role explicitly to agents

Minor point: adding a role to RELATIONSHIPS (which are already scheduled
to get a date-component). That'll also let me get at WHERE you're a
student-or-whatever, so I can add a little extra statistical weight to
graduates of Dusty's Institoot o hi-er learnin'...

'confidence score' - that seems pretty subjective.

Yes, I believe that's the point.

(audio, video should be other categories of 'how'

I'm not quite sure that's correct - it's more "behavior" or perhaps "song"

like 'photo' it's the information, not the media, that we care about -
but yes, I noticed that gap as well.

So "Cicero+Pipilo+audio" is the "baseline possible."

You can ignore the 'confidence score' (when searching and creating IDs)
for most stuff.

If you're trying to ID a bird off of a damaged tape and you just can't
quite hear enough to be sure or something, you can use 'confidence score'
as a searchable way to flag that particular ID. (And I can use your agent
info to not only get at how much I trust your IDs, but also how much I
trust your evaluation of your IDs!)

Minimally, I don't think it can detract from anything else, and it seems
that some of us have a use case for it. Ideally, perhaps it does add some
real less-subjective value in some specific situations.

We'd need to be able to apply >1 technique to an ID.

That's probably a simpler approach than my vague ideas regarding
"secondary" or "dependent" IDs. (And the "cool toys" comment in ArctosDB/internal#27
(comment)
https://github.com/ArctosDB/internal/issues/27#issuecomment-512071298
might make it trivial without mucking with the structure - not 100% sure of
that.)

Would this be one term/list, or perhaps a general+specific split - eg,

morphology; coloration; microscopy

or

general: morphology
specific: coloration; microscopy

??

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DerekSikes on 19 Jul 2019

Confidence score seems different than 'expert' versus 'non-expert' - even an expert can have a less then perfect confidence in an ID. What about something like 'certain' and 'uncertain' or something like that. Also again, 'expert' and 'non-expert' is really related to the person = agent.

---> Would this be one term/list, or perhaps a general+specific split

I'd say a list of terms, apply all that are relevant and then concatenate into a single field?

ccicero on 19 Jul 2019

I like 'certain' and 'uncertain' - I'm no expert, but I'm also fairly sure I've never misidentified a moose or walrus.... That seems to jive with Derek's use case as well.

concatenate into a single field

I think we can make that work, and if we go to https://github.com/ArctosDB/internal/issues/27#issuecomment-512071298 we can treat it as a data object (array) instead of a concatenation. (We can do that in Oracle too, but it involves creating a datatype/it's a little more complicated.)

I see no obstacles to implementation at this point, other than vocabulary.

I suggest "nature of ID" (I think we should retain that vocabulary??) remain NOT NULL with an "unknown" (=we're not ignoring this because we can, we don't know) option, and 'confidence' (??) be NULL; most of us are just not going to have that information much of the time.

@DerekSikes for migration purposes I can be as specific as the data allow - "all IDs by experts and students would be method = phenotype" isn't a problem as long as you can somehow identify "experts and students," and we can take another swing if we miss something. Going forward there would be no defaults - how you use this (and if you use it, in the case of NULLable fields) would be left to the collections.

SO - vocabulary time?

Here's Carla's list + the current vocabulary I think we need to retain and some comments.

DNA sequence - how is this not "genomics"?
genomics
morphology - "gross morphology" to distinguish from microscopy?
coloration
microscopy - I think this is somehow both too broad (karyotype should probably be it's own thing, if we still have any of that) and too narrow (eg, you could look at insect genetalia through a microscope or CT scanner). Maybe close enough for now??
audio - "call"???
video - this is tricky - probably includes calls, "gross morphology," maybe habitat, .... - IDK, maybe "video" encompasses all of that and is just right?? (Keep "audio" too for the same reasons???)
etc. - this will be a code table, we can add to it at any time, I don't think we need to anticipate everything, just get everything that we need immediately.
ID of kin
geographic distribution
unknown (née legacy)
published referral (I'm still - perhaps again - not sure I understand this - and 'type specimen' - both of which can be derived from citations attached to the identification.)

dustymc on 19 Jul 2019

Yes, this is a qualification on the identification itself, not on the
agent. As I've said, I'm an expert only on some taxa, not all, thus I use
'expert' ID only for those for which I claim expertise.

I've not argued we should be using this term to qualify the agents. I think
that's a rabbit hole of little value. These data (expert vs student) for
Identifications are just ways to state how reliable the IDs are.

If it were a field for the agent it would be in the agent table.

-D

On Thu, Jul 18, 2019 at 3:03 PM Carla Cicero notifications@github.com
wrote:

Confidence score seems different than 'expert' versus 'non-expert' - even
an expert can have a less then perfect confidence in an ID. What about
something like 'certain' and 'uncertain' or something like that. Also
again, 'expert' and 'non-expert' is really related to the person = agent.

---> Would this be one term/list, or perhaps a general+specific split

I'd say a list of terms, apply all that are relevant and then concatenate
into a single field?

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DerekSikes on 19 Jul 2019

It would be helpful to create a google doc for vocabulary and definitions to aid in migration/documentation? Can we do that please?

ccicero on 19 Jul 2019

google doc

On it....

dustymc on 19 Jul 2019

I don't like 'certain' vs 'uncertain' because certain means 100% whereas
'high confidence' means > ~90%

-D

On Thu, Jul 18, 2019 at 3:54 PM dustymc notifications@github.com wrote:

google doc

On it....

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[email protected]

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FAX: 907-474-5469

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DerekSikes on 19 Jul 2019

https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

There are two tabs - 'migration path' will remain very waffly until 'ctnature_of_id' is solidified, and will only come into play after we've dealt with whatever needs dealt with by itself (Derek's "all IDs by experts and students would be method = phenotype" and similar).

Are we agreed on "confidence" for the new field?

I'm fine with "[high|low] confidence" for the terminology, but I'm also fine with absolutely anything else that gets the idea across. Like all Arctos vocabulary, the term means precisely what we define it to mean, and using it in any way outside the definition we assign is objectively wrong.

dustymc on 19 Jul 2019

re: "I'm fine with "[high|low] confidence" for the terminology, but I'm
also fine with absolutely anything else that gets the idea across. Like all
Arctos vocabulary, the term means precisely what we define it to mean, and
using it in any way outside the definition we assign is objectively wrong."

Few users, even power users, know all the definitions (or bother to look
them up) & humans are error making machines so the more intuitive and
simple we make the terms the fewer errors will be introduced.

We could for example define "high confidence" as "confidence is low" and
then not be surprised when all the data are a mixture of confused errors.
Let's not rely on the definitions.

-Derek

On Thu, Jul 18, 2019 at 4:18 PM dustymc notifications@github.com wrote:

>

https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

There are two tabs - 'migration path' will remain very waffly until
'ctnature_of_id' is solidified, and will only come into play after we've
dealt with whatever needs dealt with by itself (Derek's "all IDs by experts
and students would be method = phenotype" and similar).

Are we agreed on "confidence" for the new field?

I'm fine with "[high|low] confidence" for the terminology, but I'm also
fine with absolutely anything else that gets the idea across. Like all
Arctos vocabulary, the term means precisely what we define it to mean, and
using it in any way outside the definition we assign is objectively wrong.

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University of Alaska Museum
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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
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http://www.uaf.edu/museum/collections/ento/
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DerekSikes on 19 Jul 2019

Obviously the terms should be as intuitive as possible, and no doubt the further we drift from that the more they're misused and data quality (eg, ability to talk to other things or answer deep questions) drops off. Avoiding confusing terminology is occasionally a decent reason to avoid all vocabulary and do something symbolic - things like 1-5 star reviews are built on this idea.

This will be applied to walrus (pretty hard to get wrong) and fossil pollen (magic, as far as I can tell) and ... - whatever we do should make some sense for anything that might end up in Arctos. I think I'm hearing that vague is better, and we should avoid any terms with numeric connotations.

"confident" and "less-confident" (and "SWAG"....)??

A sliding scale between 0 (this might not be a bird at all) and 100 (it can't possibly be anything else)??

?????

dustymc on 19 Jul 2019

--> Are we agreed on "confidence" for the new field?

Fine with me.

---> I'm fine with "[high|low] confidence" for the terminology, but I'm also fine with absolutely anything else that gets the idea across.

High/low confidence is ok with me.

ccicero on 19 Jul 2019

I just went through the google doc and made some edits to the nature of ID terms, and added a column with comments on what I did and reasons. I like it! Looking through this, I think it makes sense to just have one ID basis per ID; different bases for ID can be applied through ID history. I have not done anything yet with the migration path.

This brings up a related issue (can't find it but I think it already exists) for how to deal with multiple IDs in data entry - both individual form and bulkloader. When a specimen comes back from the field or is prepped as salvage, it's often ID'd using 'gross morphology' (previously 'field') but then another ID (geographic distribution ---> subspecies) is added when it's cataloged. We need a way to be able to enter both of these IDs and their respective 'nature of ID' at the time of cataloging.

I did find this old issue but that's not the one I'm thinking of. I'm pretty sure that I created an issue for it. Create a new issue?

ccicero on 19 Jul 2019

Agree with high low confidence. After all, IDs change, so "certain" is not
appropriate.

On Fri, Jul 19, 2019 at 7:32 AM Carla Cicero notifications@github.com
wrote:

--> Are we agreed on "confidence" for the new field?

Fine with me.

---> I'm fine with "[high|low] confidence" for the terminology, but I'm
also fine with absolutely anything else that gets the idea across.

High/low confidence is ok with me.

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campmlc on 19 Jul 2019

@ccicero thanks! Definitions look great/I'm OK with all of that.

That issue is as good as any - it's how I'll get there. PLEASE prioritize it, we can merge if anyone ever finds the other.....

dustymc on 19 Jul 2019

I'd like to make the case again for 'high' vs 'not-high' confidence and
here's why:

high = > ~90% confidence
not high = < ~ 90% confidence

low = < ~50 % confidence

not high and low mean different things. Low leaves a bunch of 'not high'
(medium?) confidence unavailable as an option.

-Derek

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@ccicero https://github.com/ccicero thanks! Definitions look great/I'm
OK with all of that.

That issue is as good as any - it's how I'll get there. PLEASE prioritize
it, we can merge if anyone ever finds the other.....

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

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DerekSikes on 19 Jul 2019

@DerekSikes OK, but I don't like 'not high' as a term. What about this:

term = identification_confidence

values:
confident: Identification is made with 90% or higher confidence.
not confident: Identification is made with less than 90% confidence.

???

ccicero on 19 Jul 2019

or

more confident: Identification is made with 90% or higher confidence.
less confident: Identification is made with less than 90% confidence.

because 89% is still fairly confident, just not quite as good as 90%.

???

ccicero on 19 Jul 2019

I think I'm digging the slider idea more and more...

If I found that 10% (or ANY percent really) of the things I'd thought were walrus were in fact not, I'd just be flabbergasted. Assigning a 90% (or 99%) confidence to that is a HUGE degradation of the data; it just doesn't remotely represent the situation, which is that there are a limited number of possible taxa that present as 5000 pound carcasses with a distinctive shape, texture, smell, and dentition on the beaches of western Alaska. Identifying walrus from ancient ivory carvings is probably a bit trickier.

On overwintered shrews from just the skull, I might start buying lottery tickets if I found out I got 90% of them right, and I don't think that's a drastically different number for "experts" - the diagnostic features just aren't there. Geneticists could certainly do much better - their "diagnostic features" don't get ground away.

I assume that sort of variability is fairly common across taxa/technique/individual, and so should be available in our evaluation of ourselves.

A slider would facilitate the full range of confidence, and also get us out of this vocabulary trap. It's an intuitive approach to this sort of data, and can be implemented through a familiar UI.

UI would look something like https://arctos.database.museum/demo - that's just the one-line, out-of-the-box implementation, it can be styled in any way.

dustymc on 19 Jul 2019

Our collection may be an outlier, but we find the distinction between "legacy," "student," and "expert" to be of value and in Dusty's table, all of them become "unknown." For us, a legacy ID (40% of our collection) is whatever arrived with the specimen. (I know that's not the exact definition in the table, but it's the closest we had to chose from.) Well over half of our lots arrive with an ID from a collector or dealer. We may have no idea what the collector's confidence level was or what the basis for the ID was, but if we haven't changed it, it is an accepted taxon name. In the ID remarks, we note if the ID has been confirmed and by whom.

A student ID (36% of our collection) is made by any and all of our volunteers as none of us is a qualified expert, but we do research the specimen and have a modest degree of confidence. Only 2% of our specimens have been reviewed by a true expert.

To me, these are important distinctions and should be to a researcher as well. I hate to have the nature of the IDs of >75% of our collection become "unknown" when we do know something about the nature, timing and quality of the ID. Are we trying to replace this information with the two options in the "degree of confidence" field? That still doesn't convey the degree of knowledge of the person making the ID (if known).

Before this is implemented, can we see a visual of how the data entry "Identification" section would look and the options in the controlled fields?

sharpphyl on 19 Jul 2019

whatever arrived with the specimen

That was the intent of legacy, and now unknown - "this is what we have."

no idea what the collector's confidence level

I think this must be a NULLable concept for precisely that reason.

In the ID remarks, we note if the ID has been confirmed and by whom.

I'm sure that's common, but it's also of extremely limited utility - it's useful for someone who's already found the specimen and is willing to read the remarks. Adding an identification makes that information much more usable.

75% of our collection become "unknown"

That's just a default. If you make generally make identifications by "gross phenotype" (or whatever) then we can use that as the default for your collection, or bits-and-pieces of it, or whatever.

Are we trying to replace this information with.... confidence

Yes, but it offers a lot more precision when that's available.

two options

Agreed, more or less - that's why I'm leaning towards something like a slider.

visual

This...

Screen Shot 2019-07-19 at 8 57 30 AM

would use terminology from https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899, and something like

https://arctos.database.museum/demo

Screen Shot 2019-07-19 at 8 58 16 AM

or some dropdown of some terms or something would be inserted near it.

dustymc on 19 Jul 2019

Missing from the last reply: Once we've established some agreeable means of recording identification_confidence, we can talk about "translating" expert, student, etc. to it. This should not be a lossy process.

dustymc on 19 Jul 2019

Should the title of this field go from Nature of ID to ID Methodology?

This does still leave out what we're eliminating from this field - the nature of the person or situation in which the ID is made: student, expert, legacy, temporary, field. Can this be captured here:

we can talk about "translating" expert, student, etc. to it. This should not be a lossy process.

And thanks for the new word for the day: lossy!

Is the Confidence-o-Meter optional?

sharpphyl on 19 Jul 2019

Nature of ID to ID Methodology?

I don't think so - this better encompasses the "basic or inherent features" of the identification - eg, someone looked at morphology. Methodology can come from id_sensu, and I'm not sure there's a lighter-weight proxy to that.

the nature of the person

That's in their agent record - eg, review Carla's publications, projects, collections, etc., and you might start to get the idea that she knows something about birds. Adding dates to relationships will eventually let you get a bit deeper in that - eg, maybe Carla's IDs made when she was an undergrad should be weighted differently.

It's also not something natural to Carla, as far as I know - I'm guessing she'd not be quite as "expert" at identifying liverworts or larval jellyfish (but who knows!) - it's just part of the context needed to evaluate a specific identification.

student

This has always been ambiguous, but some sort of lower confidence than expert should get you to one of the things it might have been intended to cover.

expert

As above.

legacy

That's just another word for "unknown" in this context.

temporary

I don't understand why this might ever exist.

field

gross phenotype I think, but I've never quite understood how this was distinct from all of our other vague terms, so...

Confidence-o-Meter

Nice!

optional

yes

I think this must be a NULLable concept for precisely that reason.

dustymc on 19 Jul 2019

I like the idea of a slide-o-meter for confidence level (which would be nullable), rather then arbitrary and more subjective categorical divisions.

I think "Nature of ID" is descriptive - to me that describes what an ID is based on, but we've been confounding it with who it was based on (expert, student) which is more appropriate in the context of agents as Dusty described.

legacy - probably 'gross phenotype' is better than unknown (?) but good question on whether that term makes sense for cultural and paleo collections. Rather than 'gross phenotype,' what about 'gross traits' to make it more broadly applicable? A basket with specific types of plant or animal matter can be described by traits, as can a fossil bone, but phenotype doesn't seem appropriate in those cases.

ccicero on 20 Jul 2019

'gross features' is better than 'gross traits' - I updated the google doc accordingly, see definition.

ccicero on 20 Jul 2019

gross features

I like it. @AJLinn

I don't much like 'related kin'==>kin kin/related relatives.

I'm wondering if we should also push 'genomics' in the direction of something like 'chemical analysis' (not crazy about that term) to encompass things like https://physicsworld.com/a/nuclear-fallout-used-to-spot-fake-art/, or if that (when/if we get those data) should be another category?

@marecaguthrie

dustymc on 20 Jul 2019

What about "trait- based" instead of " gross traits". Sometimes traits are
gross, but not always :)

We need "kin relationship" for things like captive bred wolves etc. None of
us are confirming traits when the source is a captive breeding population.

I don't think we need to go into the details of the genetic vs genomic IDs.
If we go that route, we'd have to distinguish single locus vs multilocus
(and how many loci?) nuclear vs mitochondrial or some combo thereof with
or without added morphological traits vs whole genome but which parts of
the genome etc etc. How about just "molecular"?

On Sat, Jul 20, 2019, 9:27 AM dustymc notifications@github.com wrote:

gross features

I like it. @AJLinn https://github.com/AJLinn

I don't much like 'related kin'==>kin kin/related relatives.

I'm wondering if we should also push 'genomics' in the direction of
something like 'chemical analysis' (not crazy about that term) to encompass
things like
https://physicsworld.com/a/nuclear-fallout-used-to-spot-fake-art/, or if
that (when/if we get those data) should be another category?

@marecaguthrie https://github.com/marecaguthrie

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campmlc on 20 Jul 2019

The attempted distinction is between "to the eye, it looks like a ..." and "we stuffed it under a microscope/CT scanner/etc., and there it looks like a ...."

The concept of "ID of kin" is safe, I just don't like the redundant wording - kin and relatives means about the same thing.

If single locus vs multilocus is something that users might want to search on, I have no problem adding it (now or later). If not, I think we should be as generic as possible. (I suspect 'multilocus' can only come usefully from id_sensu - a publication describing the details - and general terms are what's needed here, but ???) "Molecular" seems reasonable to me.

dustymc on 20 Jul 2019

Sorry to be out of this - I muted the thread thinking it wasn't really relevant to us as it's a field we often don't spend a lot of time thinking about, but in looking thru the google doc, I'm not seeing a lot of usefulness for cultural collections.

gross features

That term doesn't have previous meaning for cultural collections... but it's infinitely better than 'gross phenotype', which I have no idea what it means! 🥴I think we can make it work. I don't know of a better way of indicating how the ID was made that would work for all.

As Carla referenced, cultural collections people can partially ID items based on materials, but also design elements, overall form, or overall perceived function. But we make ID judgements about a variety of things (materials, culture of origin/use, copyright applicability, or even maker at times if it's not signed but looks exactly like another piece in the collection).

For cultural collections the ID field is referencing the name of the item (is it an arrow head or a spear head, is it a basket or a hat, is it a meat platter or a cutting board, a tea pot or coffee pot, a man's parka or woman's parka), which is usually directly tied to it's function. It can be complicated with objects are re-used (e.g., a leg trap spring is reused as a scraper blade or a file is turned into a knife). We get at that complexity in our attribute "description."

Most of our IDs right now are "legacy". New nature of ID labels are either curatorial (me) or student (my students doing data entry). If we have an elder come thru and correct an ID, we change it to "expert". We have lots of accidental "ID of kin" because of its default position - but I also sometimes use it intentionally with the thought: "this object looks just like another item that is IDed as a fish spear prong, so it must be a fish spear prong".

I actually wouldn't mind having a slide-o-meter for some of those other areas (attributes mostly) where we're making "educated guesses" because I'm often surprised by how clearly not-correct some of the IDs are.

I think for archaeology collections (and likely paleo as well), this is even more difficult and more important because they're looking at fragments of things. Archaeologists at our museum often come look at full-sized modern pieces in the ethnology & history collection to decide if a fragment is part of a tobacco or coffee can, or a birch bark basket rim vs. birch bark canoe top plate.

Sorry to be jumping in late and missing most of the discussion. I'm not sure how to make the nature of ID more applicable for cultural collections given these complications, but I hope you consider us in your changes. Most of the terms in the google sheet right now are not very helpful for us honestly.

AJLinn on 20 Jul 2019

---> I don't like 'trait-based' for the reasons Dusty gave. A fine count of scales or a wing measurement is also trait based, but that is different from an overall qualitative assessment based on what something looks like.

---> I've never really liked 'ID of kin' - sounds awkward to me. I do prefer 'kin relationship' even though there is slight redundancy, because I think it's clearer.

---> @AJLinn I added 'function' as a term to address your points, see definition in google doc to see if that makes sense.

Also, to address what Angela was saying about identifying cultural items based on others that look the same, I changed 'ID of kin' / 'kin relationship' to just 'relationship' so that it can apply more broadly to both cultural and natural history collections. This also makes the most sense for things like nests. Here is the definition I put in the google doc:

Identification based on the identification of a related individual (e.g., parent, sibling), a maker (e.g., for objects such as nests or cultural items), or of another object that has the same function and/or features (e.g., for cultural items).

ccicero on 20 Jul 2019

👍1

Should "fine morphology" become "fine features" (detailed features? something features...) to better contrast with "gross features"?

Maybe "general features" and "detailed features"? Qualitative features/quantitative features??

"It's obviously a teapot" is definitely what we're trying to get at with "gross features" (whatever the label ends up being).

"There are signs of percussive flaking under microscope/xray/etc., therefore it must be a Whatever Point" is "fine morphology" (again, whatever we're calling it).

"We found _Camellia sinensis_ residue on this potsherd, so it was probably a teapot" is "genomics" - the concept, we'd probably need a new label if we get those data.

Note also that the "trust factor" built into Agents doesn't live in isolation - eg if a student identifies a bunch of things, then an "expert" (eg, an agent with a bunch of relevant publications) comes through and reidentifies them, you can use the correlation between those IDs to figure out that the student is generally right (or wrong...) and use that to weight their other IDs. That's also yet another reason to create IDs when you have them instead of eg, stuffing "confirmed by {cryptic initials}" in some remarks field or something.

I like it!

dustymc on 20 Jul 2019

I had the same thought and like the contrast between 'fine' and 'gross' features - see modified description. Fine-scale analysis may be qualitative (e.g., shape of hummingbird feathers) so that contrast doesn't work. I modified the description to reflect that.

ccicero on 20 Jul 2019

genomics vs molecular: I think molecular is better. DNA sequence of cytochrome b isn't genomic, but it is molecular.

ccicero on 20 Jul 2019

minor detail - should we be consistent in adjective versus noun. e.g., 'molecules' vs 'molecular' ??? I think that would look better so changed made that change in the doc.

ccicero on 20 Jul 2019

btw, I increased the priority of this related issue to high.

ccicero on 20 Jul 2019

I don't like "molecules" - it may be semantically consistent, but it is not
in any usage in the sense of "molecular" genetics. I would advocate for
using terminology consistent with usage in the literature and in the rest
of the research and collections community.

On Thu, Jul 18, 2019 at 6:18 PM dustymc notifications@github.com wrote:

>

https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

There are two tabs - 'migration path' will remain very waffly until
'ctnature_of_id' is solidified, and will only come into play after we've
dealt with whatever needs dealt with by itself (Derek's "all IDs by experts
and students would be method = phenotype" and similar).

Are we agreed on "confidence" for the new field?

I'm fine with "[high|low] confidence" for the terminology, but I'm also
fine with absolutely anything else that gets the idea across. Like all
Arctos vocabulary, the term means precisely what we define it to mean, and
using it in any way outside the definition we assign is objectively wrong.

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campmlc on 20 Jul 2019

ok, changed it back.

ccicero on 20 Jul 2019

I made a few more comments on the google doc. Please review.

On Sat, Jul 20, 2019 at 2:47 PM Carla Cicero notifications@github.com
wrote:

ok, changed it back.

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campmlc on 20 Jul 2019

I'm not sure who changed it back to genomics, but I don't think that's accurate. What about just 'DNA' ?

'coarse features' - ok with me, nice (better) contrast with 'fine features'

'audio-visual' - yes, that's better!

ccicero on 21 Jul 2019

changed it back to genomics

Edit history says I did, but certainly not intentionally. I changed it to DNA from CC's suggestion, I'm not attached to that (or anything else, except the idea).

I'm not 100% attached to the idea, but I think there's a distinction between audio where you have only one kind of information and video where you potentially have much more. I suppose we can sort it out when we get some data...

dustymc on 21 Jul 2019

I think for the purposes of ID, audio-visual is sufficient. 'audio' could also include some behavioral aspect (observe a bird singing from the top of a juniper bush, and it sounds like an Oak Titmouse). Other information might go into 'habitat' or 'attributes' of some kind or another (and we could probably expand on attributes for behavioral data). As you said, can be sorted out later.

This brings up another point for the purposes of migration: basis of record will be important, because how data are migrated will depend on context (observation, preserved specimen, cultural item, etc.). For example, I would say that all bird observations with a 'field' nature of ID and an associated media would be changed to "audio-visual' - we should modify the migration tab to incorporate this somehow.

ccicero on 21 Jul 2019

I like where this is going and moving away from subjective expert vs. non-expert descriptors. I am ok with adding a slider but I propose we style it in a way that doesn't give false-precision to the confidence value (is 63% confidence significantly more meaningful than 65%? How do you determine this anyway?). Perhaps there can be intervals - enough so that we aren't degrading the data but not so many so as to drive ourselves nuts fretting over the minutia (e.g. 100%, >90%, >80% 70-50%,,<50% .... or something). When we have an expert redetermine or confirm ID for loans, do we unrealistically ask them to rate their confidence? When they don't include their confidence ratings do we leave this field null despite the fact we know the specimens have been examined by a specialist? Or do we introduce some level of educated interepretation (>80%?)? If so, I think ranges vs. straight integers allows us to accurately convey confidence without getting overly precise.

ebraker on 22 Jul 2019

As long as I can leave the rating slider null (not zero, NULL), I don't care, because I am not going to make any judgement calls about the relative expertise of anyone's ID (nor do I want to have the person who made the ID rate themselves). The move to objective means of identification is awesome an I totally support it.

Jegelewicz on 22 Jul 2019

I think much of that's documentation??

I can round to any precision....

UAM@ARCTOS> select round(45.9995476788,-1) from dual;

ROUND(45.9995476788,-1)
-----------------------
             50

but that might be more misleading/confusing.

At some point the ID (and probably specimen) bulkloader will likely need to accept a NUMBER and downloads will contain a NUMBER as well; we have limited control over UI.

The documentation should stress that this is a subjective thing which should be set to "that feels about right."

Any query access will need carefully and similarly documented; most of these data will be NULL, and so setting this to any value will exclude most specimens. I don't think it will be useful for "normal" specimen searches, it will be used by "us" to find the situations we created by using the tool.

I'm inclined to just accept whatever I'm given (within some defined range), mostly because I think it's least confusing. I suppose if someone really wants to set up some distinction between 89.00000345 and 89.00000346 they can, all we can do it make the documentation clear....

dustymc on 22 Jul 2019

I changed back to "molecular" because this can include proteins,
immunology, RNA, future tech we don't know about yet . . . Otherwise we
have to specify each one . . .

On Sat, Jul 20, 2019 at 6:43 PM dustymc notifications@github.com wrote:

changed it back to genomics

Edit history says I did, but certainly not intentionally. I changed it to
DNA from CC's suggestion, I'm not attached to that (or anything else,
except the idea).

I'm not 100% attached to the idea, but I think there's a distinction
between audio where you have only one kind of information and video where
you potentially have much more. I suppose we can sort it out when we get
some data...

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campmlc on 22 Jul 2019

I'm not a fan of the slider concept. How are students going to use this in
data entry? How do we assign in the field on a rapid assembly line? What
does it mean, anyway? It seems most useful for specimens that have been
subsequently examined curatorially to indicate if something has indeed been
examined by an expert on that particular taxonomic group. Everything else
by anyone else is "not enough info to assess confidence".

On Mon, Jul 22, 2019 at 10:38 AM Mariel Campbell campbell@carachupa.org
wrote:

I changed back to "molecular" because this can include proteins,
immunology, RNA, future tech we don't know about yet . . . Otherwise we
have to specify each one . . .

On Sat, Jul 20, 2019 at 6:43 PM dustymc notifications@github.com wrote:

changed it back to genomics

Edit history says I did, but certainly not intentionally. I changed it to
DNA from CC's suggestion, I'm not attached to that (or anything else,
except the idea).

I'm not 100% attached to the idea, but I think there's a distinction
between audio where you have only one kind of information and video where
you potentially have much more. I suppose we can sort it out when we get
some data...

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campmlc on 22 Jul 2019

include proteins, immunology, RNA, future tech we don't know about yet. . . Otherwise we have to specify each one . . .

This is a question for users, but perhaps specifying each one is important - eg, species hypotheses built on "future tech we don't know about yet" [do|do not] align with species hypotheses built on {something else} and users will want to find those specimens and request loans.

Or we could see this as a not-so-precise category and get at "future tech we don't know about yet" via id_sensu (publications).

I think one category, whatever we call it, is probably OK for now, just something to keep in mind...

I'm not a fan of the slider concept.

So don't use it.

What does it mean, anyway?

By definition, probably something like 'subjective measure of how confident the identifier is in the identification." By usage, whatever Curators want it to mean...

It provides a pathway to get at the things Derek mentioned without engaging in an endless vocabulary debate, and it does it without requiring anything from anyone who doesn't want to use it or taking anything of value from identifications which haven't specified a 'confidence.'

"not enough info to assess confidence"

That's NULL, which would be the default condition.

dustymc on 22 Jul 2019

I imagine using NULL in the majority of cases for our collection so I am not all out opposed to the slider. That said, I wonder if it is more straightforward to have some sort of toggle, e.g., "ID tentative" rather than attempting to quantify the degree of uncertainty for an identification in an unmethodical way across multiple collection types and personal assertion styles (and essentially reintroducing subjectivity, e.g., 80 vs 85% cetain). A flagged record could still be elaboarated upon with a textual description (or alas, even a numeric rating) in the ID_remarks if desired and is easily searched. It just seems like if we create some sort of Confidence-o-Meter and then find a better structure down the line, we then have to migrate all of these [overly] precise values into the new model that hold varying degrees of meaningfulness and which will likely be interpreted as [overly] significant for future users. For me, just knowing an ID is uncertain is valuable - regardless of whether the determiner was 80% or 45% confident, I know that specimens needs further examination and should likely be excluded from niche models, etc.

ebraker on 22 Jul 2019

I prefer Emily's alternative to the slider.

As for:
get at "future tech we don't know about yet" via id_sensu (publications)

Yes, we just need to rely on liking to the publication. It is hard enough
for curatorial staff to just find and link publications. To add a
requirement that we read through the entire methods section of each pub to
figure out exactly what technique they used and translate that into some
Arctos terminology would not be reasonable. It is hard enough for me to
find those studies just based on "genetic" or "molecular" vs "morphology".
Parsing it further would require an enormous amount of time and effort.

On Mon, Jul 22, 2019 at 11:03 AM Emily Braker notifications@github.com
wrote:

I imagine using NULL in the majority of cases for our collection so I am
not all out opposed to the slider. That said, I wonder if it is more
straightforward to have some sort of toggle, e.g., "ID tentative" rather
than attempting to quantify the degree of uncertainty for an identification
in an unmethodical way across multiple collection types and personal
assertion styles (and essentially reintroducing subjectivity, e.g., 80 vs
85% cetain). A flagged record could still be elaboarated upon with a
textual description (or alas, even a numeric rating) in the ID_remarks if
desired and is easily searched. It just seems like if we create some sort
of Confidence-o-Meter and then find a better structure down the line, we
then have to migrate all of these [overly] precise values into the new
model that hold varying degrees of meaningfulness and which will likely be
interpreted as [overly] significant for future users. For me, just knowing
an ID is uncertain is valuable - regardless of whether the determiner was
80% or 45% confident, I know that specimens needs further examination and
should likely be excluded from niche models.

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campmlc on 22 Jul 2019

toggle, e.g., "ID tentative"

I'm certainly fine with that, but it didn't look like we were headed for vocabulary resolution above. Something symbolic (slider, stars, whatever) doesn't require us to define terms - that's essentially all of my "recommendation." Derek seems to the the one with a solid use case; I'm happy enough to do whatever he tells me to do, as long as nobody else is screaming too loudly....

ID_remarks

No free-text field anywhere is usefully searchable, at least not as long as we let humans provide the values. Wee maek typograaphical eerors n etc....

It is hard enough for curatorial staff to just find and link publications.

I don't doubt that, but it provides a level of precision that nothing else can. It's certainly never going to be anything like a requirement, but if it's there it becomes a powerful tool that users can access for all sorts of reasons; it makes your data more able to answer more questions.

entire methods section of each pub to figure out exactly what technique they used and translate

That would be (can be now) up to the user, not "us." Any translation would be a downgrade. Maybe users want specimens IDed genetically using some primer that they don't trust - they can get that from id_sensu, it's not something we'd realistically be able to to predict, summarize, and/or categorize.

"genetic" or "molecular"

Those two values in the same list would probably lead to ambiguous usage.

dustymc on 22 Jul 2019

I've been considering the slider idea and have fears there will be
unforeseen undesirable consequences. Mariel brought one up I hadn't
considered - how to bulkload the data? Also, how do we search on the field
if we don't know what's in it? or would a value 0-100 appear as the slider
is set? We could then search on those values?

I still think this brings in massive over-precision. I might set a value of
85 one day and 87 another and 90 or 86 another day all for the same basic
ID job.. it's asking users to split hairs and make impossible decisions.
Even if we just had the scale run from 1-10 (an improvement) it would still
be hard to decide.

I really like a binary choice - is this a reliable ID or not? (or null for
unknown)

-Derek

On Mon, Jul 22, 2019 at 9:30 AM dustymc notifications@github.com wrote:

toggle, e.g., "ID tentative"

I'm certainly fine with that, but it didn't look like we were headed for
vocabulary resolution above. Something symbolic (slider, stars, whatever)
doesn't require us to define terms - that's essentially all of my
"recommendation." Derek seems to the the one with a solid use case; I'm
happy enough to do whatever he tells me to do, as long as nobody else is
screaming too loudly....

ID_remarks

No free-text field anywhere is usefully searchable, at least not as long
as we let humans provide the values. Wee maek typograaphical eerors n
etc....

It is hard enough for curatorial staff to just find and link publications.

I don't doubt that, but it provides a level of precision that nothing else
can. It's certainly never going to be anything like a requirement, but if
it's there it becomes a powerful tool that users can access for all sorts
of reasons; it makes your data more able to answer more questions.

entire methods section of each pub to figure out exactly what technique
they used and translate

That would be (can be now) up to the user, not "us." Any translation would
be a downgrade. Maybe users want specimens IDed genetically using some
primer that they don't trust - they can get that from id_sensu, it's not
something we'd realistically be able to to predict, summarize, and/or
categorize.

"genetic" or "molecular"

Those two values in the same list would probably lead to ambiguous usage.

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DerekSikes on 22 Jul 2019

how to bulkload the data?

The slider would just be an abstraction of some range of values - 0-1 or 0-10000000000 or whatever - I think it's become "percent confidence" in my head but that's probably overly precise/wrong.

Arctos is unicode, so something like a code table of

IN (NULL,⭐,⭐⭐,⭐⭐⭐,⭐⭐⭐⭐,⭐⭐⭐⭐⭐)

is completely possible as well. Not suggesting we should, but we could - we are not limited to text/ASCII.

I might set a value of 85 one day and 87 another and 90 or 86 another day all for the same basic
ID job.

Yep, probably - I guess in addition to the terminology thing, you (or someone) mentioned some "expert" threshold above that sounded really low for some use cases. The slider would let you-the-user and you-the-operator define "expert" (or "unreliable" or whatever) however you want, assuming there's some sort of grouping around sliding the widget ALMOST all the way to the right for "I'm pretty confident in this" - and that may be an unjustified assumption.

binary

I'm certainly fine with that if we can find acceptable vocabulary. It's a lot easier to code too!

null for unknown

It's overly pedantic for this conversation, but those are not the same thing. NULL ==> we say nothing (including about why we're saying nothing). "Unknown" ==> we don't have the information. (https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE contains a couple more ways we can get at not having anything to say.)

dustymc on 22 Jul 2019

null for unknown
It's overly pedantic for this conversation, but those are not the same thing. NULL ==> we say nothing (including about why we're saying nothing). "Unknown" ==> we don't have the information. (https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE contains a couple more ways we can get at not having anything to say.)

I think it is an important distinction...

Jegelewicz on 22 Jul 2019

agree.

On Mon, Jul 22, 2019 at 1:00 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

null for unknown

It's overly pedantic for this conversation, but those are not the same
thing. NULL ==> we say nothing (including about why we're saying nothing).
"Unknown" ==> we don't have the information. (
https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE
contains a couple more ways we can get at not having anything to say.)

I think it is an important distinction...

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campmlc on 22 Jul 2019

Agreed

4 options for ID confidence, how about:

reliable
uncertain reliability
unknown
NULL

I really think we should avoid making clear statements that the reliability
is poor or unreliable etc. because that seems too strong & we don't want to
be making former nature of IDs with 'student' = 'unreliable'... a much
better term is ' uncertain reliability'

-D

On Mon, Jul 22, 2019 at 11:00 AM Teresa Mayfield-Meyer <
[email protected]> wrote:

null for unknown

It's overly pedantic for this conversation, but those are not the same
thing. NULL ==> we say nothing (including about why we're saying nothing).
"Unknown" ==> we don't have the information. (
https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE
contains a couple more ways we can get at not having anything to say.)

I think it is an important distinction...

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DerekSikes on 22 Jul 2019

I'm OK with that, but there have also been times when I might have used an "unreliable" option. Something's not some Eurasian species so I know more than genus (the next-highest taxonomic pigeonhole), but I'm still not entirely confident that the species I've picked is correct. I suppose "A {string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain reliability" and "unknown" (and NULL) - I'm not sure I see that just from the vocabulary.

dustymc on 22 Jul 2019

Perhaps we need to treat these as flags going forward, but legacy data will
have to be left as null. I would not want to convert all our "student" IDs
to uncertain reliability if that meant those records would be excluded from
niche modeling, for example. Most everything we have is "student".

On Mon, Jul 22, 2019 at 1:15 PM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used an
"unreliable" option. Something's not some Eurasian species so I know more
than genus (the next-highest taxonomic pigeonhole), but I'm still not
entirely confident that the species I've picked is correct. I suppose "A
{string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain
reliability" and "unknown" (and NULL) - I'm not sure I see that just from
the vocabulary.

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campmlc on 22 Jul 2019

I keep forgetting to mention this but in that case, when you want to
indicate unreliable, why not just use ID formula A ?

-D

On Mon, Jul 22, 2019 at 11:15 AM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used an
"unreliable" option. Something's not some Eurasian species so I know more
than genus (the next-highest taxonomic pigeonhole), but I'm still not
entirely confident that the species I've picked is correct. I suppose "A
{string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain
reliability" and "unknown" (and NULL) - I'm not sure I see that just from
the vocabulary.

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[email protected]

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FAX: 907-474-5469

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DerekSikes on 22 Jul 2019

Mariel,

If we did go this route then it sounds like you'd like your 'student' IDs
changed to 'reliable' ? I suppose Dusty could do this on a case-by case
basis. But then how would you distinguish 'world expert/taxonomic
authority' based IDs from the rest in your collection?

-Derek

On Mon, Jul 22, 2019 at 11:17 AM Mariel Campbell notifications@github.com
wrote:

Perhaps we need to treat these as flags going forward, but legacy data will
have to be left as null. I would not want to convert all our "student" IDs
to uncertain reliability if that meant those records would be excluded from
niche modeling, for example. Most everything we have is "student".

On Mon, Jul 22, 2019 at 1:15 PM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used
an
"unreliable" option. Something's not some Eurasian species so I know more
than genus (the next-highest taxonomic pigeonhole), but I'm still not
entirely confident that the species I've picked is correct. I suppose "A
{string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain
reliability" and "unknown" (and NULL) - I'm not sure I see that just from
the vocabulary.

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University of Alaska Museum
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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
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DerekSikes on 22 Jul 2019

We have expert for some of our IDs made by experts in that group who have
examined the specimens through some criteria. But most of our IDs are made
by collection managers who use "student" because they are not experts in a
particular group, even though they are qualified taxonomic professionals.
This is what we've been instructed to consider "student" to mean.
Even our "field" IDs are usually made by people who are consulting keys and
have some knowledge of the taxa involved - but we are missing key
characters (e.g. cleaned dentition) to make a full diagnosis; and the
confidence depends largely on the species richness and geographic
distribution of the taxonomic group at a particular locality . . .

On Mon, Jul 22, 2019 at 1:21 PM DerekSikes notifications@github.com wrote:

Mariel,

If we did go this route then it sounds like you'd like your 'student' IDs
changed to 'reliable' ? I suppose Dusty could do this on a case-by case
basis. But then how would you distinguish 'world expert/taxonomic
authority' based IDs from the rest in your collection?

-Derek

On Mon, Jul 22, 2019 at 11:17 AM Mariel Campbell >
wrote:

Perhaps we need to treat these as flags going forward, but legacy data
will
have to be left as null. I would not want to convert all our "student"
IDs
to uncertain reliability if that meant those records would be excluded
from
niche modeling, for example. Most everything we have is "student".

On Mon, Jul 22, 2019 at 1:15 PM dustymc notifications@github.com
wrote:

I'm OK with that, but there have also been times when I might have used
an
"unreliable" option. Something's not some Eurasian species so I know
more
than genus (the next-highest taxonomic pigeonhole), but I'm still not
entirely confident that the species I've picked is correct. I suppose
"A
{string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain
reliability" and "unknown" (and NULL) - I'm not sure I see that just
from
the vocabulary.

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FAX: 907-474-5469

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campmlc on 22 Jul 2019

Was just typing what Derek said re: formula A ?. A slider also wouldn't convey that you are certain about genus designation, still wavering between a couple species but can confidently rule out all Eurasian taxa in a given group. The pick list: reliable/certain, unreliable/tentative, unknown, null (or whatever values we choose) would be an intuitve way to flag records without having to think too hard as well as a means to conviently call up records with uncertain IDs in a search. ID_remarks and/or formulas would then further detail the thinking behind tentative determinations.

If we decide to map all student IDs to NULL, perhaps we can integrate the confidence flag into the Manage menu. That way we could do global updates for taxa (yes, all skulls identified as Alces alces are reliably moose) or by agent (yes, this collection manager or grad student is good for bird IDs) or whatever parameter. I will very likely leave current student values NULL and make opportunistic changes when I happen upon them, but would use the flag moving forward for new records.

ebraker on 22 Jul 2019

legacy data will have to be left as null

I can deal with that by collection (or any other criteria ya'll want to put together). I don't think anything global will or should happen. Pushing some confidence value for CollectionA 'expert' IDs and doing something different in CollectionB and ..... isn't much of a problem, and I think hinges on how the existing values have been used up to this point. I'm pretty sure we can do this without losing anything or forcing anyone in any direction they don't want to go in.

meant those records would be excluded from niche modeling,

We obviously can't control how people use data, but I can't really see why anyone would want to do that.

The flag doesn't/can't say anything about the ID, it's just how confident a particular user is in a particular ID. My "oh yea, I think I totally nailed it" is (in light of my "expertise" via my agent record and perhaps my cited publication) almost certainly of less value than Derek's "I'm not very sure about this" on the same beetle, for instance. This field does not and cannot live in isolation, and it should not be seen that way.

why not just use ID formula A

... {string} presumably. Searchability - if you CAN mis-type strings, you WILL mis-type strings, so it's not as discoverable in certain search fields. You can still search by the taxonomy component - I suppose you could mix all that up to say "I'm leaning towards Sorex tundrensis" (ID to species, low confidence) or "it's definitely one of the northern tricolored shrews (ID to genus, a bit more info via the text-based ID, high confidence).

dustymc on 22 Jul 2019

Rather than 'reliable' and 'uncertain reliability' which sounds really awkward to me and am not sure what it really means or how to use it, what about this:

ID certain
ID uncertain
ID certainty unknown
null

ccicero on 22 Jul 2019

Hate to belabor this but I keep worrying about us stating falsehoods.

ID certain is not the same as ID reliable.

The former means 100% - error is impossible, the latter means it's
trustworthy but of course, humans being humans...

so if we don't use 'reliable' I hope we can find an actual synonym

-Derek

On Mon, Jul 22, 2019 at 12:20 PM Carla Cicero notifications@github.com
wrote:

Rather than 'reliable' and 'uncertain reliability' which sounds really
awkward to me and am not sure what it really means or how to use it, what
about this:

ID certain
ID uncertain
ID certainty unknown
null

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University of Alaska Museum
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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

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DerekSikes on 22 Jul 2019

I think we moved away from certain because it implies immutability?

On Mon, Jul 22, 2019, 2:20 PM Carla Cicero notifications@github.com wrote:

Rather than 'reliable' and 'uncertain reliability' which sounds really
awkward to me and am not sure what it really means or how to use it, what
about this:

ID certain
ID uncertain
ID certainty unknown
null

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campmlc on 22 Jul 2019

As above, "ID _bla_" should be taken to mean "the person(s) making this identification say they're _bla_ of it" and not, ever, under any circumstances, "this identification is actually _bla_." I think we're trying to put meaning that can't exist into this.

dustymc on 22 Jul 2019

If the person making the IDs is also the person entering the ID data into
Arctos we can say "I'm certain/uncertain" of it but in many cases we're
entering IDs made by others... and we still want some way to say how
reliable the IDs are and 'certain' shouldn't be an option.

-D

On Mon, Jul 22, 2019 at 1:08 PM dustymc notifications@github.com wrote:

As above, "ID bla" should be taken to mean "the person(s) making this
identification say they're bla of it" and not, ever, under any
circumstances, "this identification is actually bla." I think we're
trying to put meaning that can't exist into this.

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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
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DerekSikes on 22 Jul 2019

How about:
field: "ID confidence"
values: high, medium, low, unknown, null

On Mon, Jul 22, 2019 at 3:08 PM dustymc notifications@github.com wrote:

As above, "ID bla" should be taken to mean "the person(s) making this
identification say they're bla of it" and not, ever, under any
circumstances, "this identification is actually bla." I think we're
trying to put meaning that can't exist into this.

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campmlc on 22 Jul 2019

I'm ok with these... but to which would 'student' map? medium? or low? (or
let each collection decide which)

Rarely an expert will return specimens with a ? next to the ID. How would
we record this? ID confidence = high but use ID formula A ?

-D

On Mon, Jul 22, 2019 at 1:19 PM Mariel Campbell notifications@github.com
wrote:

How about:
field: "ID confidence"
values: high, medium, low, unknown, null

On Mon, Jul 22, 2019 at 3:08 PM dustymc notifications@github.com wrote:

As above, "ID bla" should be taken to mean "the person(s) making this
identification say they're bla of it" and not, ever, under any
circumstances, "this identification is actually bla." I think we're
trying to put meaning that can't exist into this.

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DerekSikes on 22 Jul 2019

or let each collection decide which

Yes - and if a particular collection also wants THAT student to "medium" and THIS one to "low" and some other to NULL I can accommodate that too.

? next to the ID

Ideally you'd ask them (eg, by way of sending them some form that you can upload to Arctos), but if you're assigning things you can obviously do whatever you think they meant or just leave confidence NULL. "I'm sure it might be that" certainly fits....

dustymc on 22 Jul 2019

Ok, are we good with Mariel's suggestion?

field: "ID confidence"
values: high, medium, low, unknown, null

-D

On Mon, Jul 22, 2019 at 1:58 PM dustymc notifications@github.com wrote:

or let each collection decide which

Yes - and if a particular collection also wants THAT student to "medium"
and THIS one to "low" and some other to NULL I can accommodate that too.

? next to the ID

Ideally you'd ask them (eg, by way of sending them some form that you can
upload to Arctos), but if you're assigning things you can obviously do
whatever you think they meant or just leave confidence NULL. "I'm sure it
might be that" certainly fits....

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DerekSikes on 23 Jul 2019

👍1

I'm fine with that.

ccicero on 23 Jul 2019

Are we good to go with this? If so I can

add "identification_confidence" using...
- high==>Determiner(s), or collection personnel on behalf of determiners(s), have high confidence that the identification is correct.
- medium==>Determiner(s), or collection personnel on behalf of determiners(s), have moderate confidence that the identification is correct.
- low==>Determiner(s), or collection personnel on behalf of determiners(s), have low confidence that the identification is correct.
- unknown==>Determiner(s), or collection personnel on behalf of determiners(s), have expressed that they do not know how confident the identification is.
- (NULL==>nobody asserts anything)
add the values from the spreadsheet to the code table
set up a temporary trigger to disallow using 'old' values
work with ya'll to migrate existing data to the new structure
clean up old values

From https://github.com/ArctosDB/arctos/issues/1868: When implementing add drag-drop ordering, replace the JS checks with HTML5 controls

dustymc on 24 Jul 2019

Could we change "Identifier(s)" to "Determiners"

The latter is a synonym of the former but the former is a homonym of those
numbers and codes we assign to specimens... and homonyms can lead to
confusions.

Otherwise, I'm happy with this.

-Derek

On Wed, Jul 24, 2019 at 12:19 PM dustymc notifications@github.com wrote:

Are we good to go with this? If so I can

add "identification_confidence" using...

high==>Identifier(s), or collection personnel on behalf of

identifier(s), have high confidence that the identification is correct.

medium==>Identifier(s), or collection personnel on behalf of

identifier(s), have moderate confidence that the identification is correct.

low==>Identifier(s), or collection personnel on behalf of

identifier(s), have low confidence that the identification is correct.

unknown==>Identifier(s), or collection personnel on behalf of

identifier(s), have expressed that they do not know how confident the

identification is.

(NULL==>nobody asserts anything)

add the values from the spreadsheet
https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899
to the code table

set up a temporary trigger to disallow using 'old' values

work with ya'll to migrate existing data to the new structure

clean up old values

From #1868 https://github.com/ArctosDB/arctos/issues/1868: When
implementing add drag-drop ordering, replace the JS checks with HTML5
controls

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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

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http://www.uaf.edu/museum/collections/ento/
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DerekSikes on 24 Jul 2019

👍1

Determiners

Edited above.

dustymc on 24 Jul 2019

What about saying that high confidence means high confidence that the
determiner asserts that the identification is correct according to
currently accepted taxonomy?

On Wed, Jul 24, 2019 at 3:22 PM dustymc notifications@github.com wrote:

Determiners

Edited above.

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campmlc on 24 Jul 2019

according to...taxonomy

That's what ID_Sensu does, and confounding it with something else could only result in conflicting and low-quality data.

dustymc on 25 Jul 2019

I'm ok with the confidence score.

Are we settled on the vocabulary? I'm still strugging with 'fine features' and 'coarse features' - I like the contrast, but it just sounds funny to me when applied to birds and isn't really clear without reading the definition. Can we think of something better that works for cultural as well as natural history specimens? Can we use 'fine traits' and 'coarse traits' instead? We use trait-based data all the time, and I think (?) that is clearer for natural history phenotypic information but does it work for cultural collections @AJLinn ?

We need to work on the migration path.

ccicero on 25 Jul 2019

fine features' and 'coarse features'

It's not COMPLETELY painless, but changing vocabulary, as long as we're not altering the concept/meaning, isn't too difficult. I'm not thrilled with the current vocab either, but I think it sufficiently says what we're trying to get across.

I think "trait" may in some communities be tainted with the implication of precise measurements, but otherwise I like it....

I've made some minor updates to the migration tab on the spreadsheet. Again this will be a "it's been X time and nobody's contacted me" fallback; I will work with anyone who wants to to bring their data across in non-default ways, and the path I've laid out above doesn't require us to do that before moving to the new vocabulary/structure. I can also retain the old values in remarks, so we can revisit anything that didn't get migrated as it should have.

FWIW in looking for "ID of kin" I scrolled by "relationship" about 8 times - perhaps that term could still use some help (or maybe it's just me...).

dustymc on 25 Jul 2019

For ID of kin, there may not be an explicitly stated relationship to another individual. The relationship may be to others in a captive breeding population, and we only have some of those individuals cataloged in Arctos, and we don't have all the familiar relationships tracked.

campmlc on 25 Jul 2019

I can't readily enforce such things (and don't really want to), but without a relationship the 'relationship' identification is less than useless. We are asserting that this is the same as something else, but you can't have any of that because we're not going to tell you what it is. I very strongly recommend we add the caution regarding relationships back to the documentation.

I don't think any of the reasons given are barriers - nests and eggs can be cataloged and referenced, sightings can be cataloged as observations, reference material in other collections can be linked (or at least given IDs, which will presumably become links when the other collection gets better technology), etc.

In the case @campmlc mentioned, I'd probably use 'unknown' and elaborate in remarks: "This specimen was not examined, but it is the sibling of ABCXYZ which was examined using......"

dustymc on 25 Jul 2019

Can we use 'fine traits' and 'coarse traits' instead? We use trait-based data all the time, and I think (?) that is clearer for natural history phenotypic information but does it work for cultural collections @AJLinn ?

"Traits" instead of "features" should be fine for us. Any of these new changes will require some re-training, but that's just fine with me if it gives us more clear explanations! Just curious... if we go thru and make changes/updates to the nature of ID based on these new categories, does Arctos retain a history of those changes so we can see "it used to be IDed as a toggle but someone with a high confidence changed it to be a belt fastener on this date"? I assume so, but I don't know how to get at that info.

AJLinn on 25 Jul 2019

@AJLinn ID history is preserved, but the old terminology will only be preserved in remarks.

http://arctos.database.museum/guid/MSB:Mamm:55245 has a bunch of IDs, all in agreement with each other.

Screen Shot 2019-07-25 at 9 55 25 AM

I can certainly 'unaccept' the current ID and add one as part of the migration process if that's somehow useful to you.

dustymc on 25 Jul 2019

@AJLinn ID history is preserved, but the old terminology will only be preserved in remarks.

http://arctos.database.museum/guid/MSB:Mamm:55245 has a bunch of IDs, all in agreement with each other.

In that example, those additional IDs were inserted by "Add Determination", right? Is there a best practice for making changes, by "Edit an Existing Determination" vs. "Add Determination"? Will the most current & highest confidence be privileged over the later, lower confidence ID if they're just added vs. editing? If we use edit to change, we would manually enter the change history in remarks?

AJLinn on 25 Jul 2019

inserted by "Add Determination", right?

Yes, same pathway/structure anyway - they were likely created with the citation bulkloader.

"Edit an Existing Determination" vs. "Add Determination"

If you're not changing anything fundamental, edit is probably OK. If you're changing something fundamental, or adding new opinions (including those that agree with current opinions), add is better. I don't think adding can ever be "wrong."

You can choose "accept" (or not) when creating an ID. A new accepted will push everything else to unaccepted; nothing manual is required.

You can explicitly choose which ID is accepted - eg, keeping an older or lower-confidence ID as accepted is fine, that's 100% a curatorial call.

dustymc on 25 Jul 2019

👍1

I'm going to next task and implement per https://github.com/ArctosDB/arctos/issues/2170#issuecomment-514784485 unless someone stops me soonish, lest this falls through the cracks again.

dustymc on 26 Aug 2019

The table structure is in place and the single-record form can access identification_confidence. I'll get the other Arctos forms next.

After that I'll add https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899 to the code table, and then I intend to disallow usage of existing terms - I can't just get rid of them until we've migrated everything. That's probably going to be a bit disruptive for things currently in the bulkloader - please let me know if I can help update anything.

Can we NOT implement identification_confidence in the bulkloader for the time being? It should be there, but if there is not an immediate need I would like to delay that until we get to a new system so I don't have to rebuild a huge amount of complex code in two languages. If there is an immediate need I'll just deal with it.

dustymc on 2 Oct 2019

"legacy terms" are now blocked from new ~usage~ insert; they can still be used for update (necessary to allow adding identifications, which implicitly updates all existing IDs). I'm increasing priority of this; the longer we put off finalizing migration, the more chances that will have to cause problems.

/remind me, check back in two weeks

I am taking migration requests. I'll do something hopefully-not-too-random (and leave verbose remarks) with the legacy data if I don't receive specific instructions in the next two weeks.

Here's a very tentative plan. Please let me know if I can make any of these updates globally (for all identifications in all collections) now; some seem straightforward, but perhaps I'm missing something.

ID of kin --> relationship
ID to species group --> unknown
curatorial --> unknown
erroneous citation --> unknown
expert --> unknown
field --> unknown
legacy --> unknown - CAN I DO THIS NOW?
molecular data--> molecular - CAN I DO THIS NOW?
photograph --> unknown
published referral --> unknown
~revised taxonomy --> taxonomic revision - CAN I DO THIS NOW?~
student --> unknown
type specimen --> unknown

dustymc on 2 Oct 2019

Dusty,

I need all the IDs in my collections with nature of id 'expert' ->
confidence = 'high'

& why are you planning on changing 'revised taxonomy' back to 'taxonomic
revision'????? We changed 'taxonomic revision' to 'revised taxonomy' for
very good reasons!! They should stay 'revised taxonomy'!!

Re: molecular data-> molecular.... sure, why not

re: legacy-> unknown .... I suppose so.

I also want all my nature of id 'student' to have confidence = medium

& nature of ID 'type specimen' should not become 'unknown' !! those are the
HIGHEST confidence IDs we can possibly have, since the name they are given
is correct, by definition.

-Derek

On Wed, Oct 2, 2019 at 10:55 AM dustymc notifications@github.com wrote:

"legacy terms" are now blocked from new usage insert; they can still be
used for update (necessary to allow adding identifications, which
implicitly updates all existing IDs). I'm increasing priority of this; the
longer we put off finalizing migration, the more chances that will have to
cause problems.

!remind me, check back in two weeks

I am taking migration requests. I'll do something hopefully-not-too-random
(and leave verbose remarks) with the legacy data if I don't receive
specific instructions in the next two weeks.

Here's a very tentative plan. Please let me know if I can make any of
these updates globally (for all identifications in all collections) now;
some seem straightforward, but perhaps I'm missing something.

ID of kin --> relationship
ID to species group --> unknown
curatorial --> unknown
erroneous citation --> unknown
expert --> unknown
field --> unknown
legacy --> unknown - CAN I DO THIS NOW?
molecular data--> molecular - CAN I DO THIS NOW?
photograph --> unknown
published referral --> unknown
revised taxonomy --> taxonomic revision - CAN I DO THIS NOW?
student --> unknown
type specimen --> unknown

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University of Alaska Museum
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[email protected]

phone: 907-474-6278
FAX: 907-474-5469

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http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
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DerekSikes on 2 Oct 2019

nature of id 'expert' ->confidence = 'high'

I need a new value for nature - that's not a change, it's an addition.

nature of id 'student' to have confidence = medium

ditto

hanging 'revised taxonomy' back to 'taxonomic revision'?????

That's what's in the spreadsheet: https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

'type specimen' should not become 'unknown' !!

What should they become then? _I_ certainly don't know how they were made!

HIGHEST confidence

That's a separate issue. "We don't know where this came from (nature_of_id=unknown), but it can't possibly be wrong (confidence=high)" fits in the new model.

dustymc on 2 Oct 2019

D,

I just don't want to lose nature of ID = expert BEFORE we set confidence
for those IDs to High, otherwise, how would we do so??

& ditto for nature of ID = student

Re: revised taxonomy.... what argument was made to change this back to
taxonomic revision?? I'm sure there's a record of all the discussion on
this but in a nutshell, 'revised taxonomy' is better because the term
'revision' has a specific meaning in taxonomy and not all taxonomic changes
come from taxonomic revisions. Thus it is confusing and misleading to use
'taxonomic revision'. Change the table.

re: type specimens - if we don't want to keep this in nature of ID then it
should be in the confidence field. It would represent a step above 'high',
at least for primary types... My concern is there must be specimens with
nature of ID = type specimen that are not linked to publications via a
citation as 'types' & thus we'll loose this information. Perhaps it should
be added to ID remarks to ensure it's not lost?

-Derek

On Wed, Oct 2, 2019 at 11:07 AM dustymc notifications@github.com wrote:

nature of id 'expert' ->confidence = 'high'

I need a new value for nature - that's not a change, it's an addition.

nature of id 'student' to have confidence = medium

ditto

hanging 'revised taxonomy' back to 'taxonomic revision'?????

That's what's in the spreadsheet:
https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

'type specimen' should not become 'unknown' !!

What should they become then? I certainly don't know how they were made!

HIGHEST confidence

That's a separate issue. "We don't know where this came from
(nature_of_id=unknown), but it can't possibly be wrong (confidence=high)"
fits in the new model.

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
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DerekSikes on 2 Oct 2019

D - I'd prefer to set them all at once so they don't have an opportunity to get mixed up with any 'legacy' values.

UPDATE identification SET nature=newthing, confidence=whatever WHERE {anything I can get from existing data - collection, agent, nature, dates, publications, whatever}

is my strong preference.

revised taxonomy.... what argument

I have none - I'm just copying from the spreadsheet!

My concern is there must be specimens with
nature of ID = type specimen that are not linked to publications via a
citation as 'types'

Very possible, and I'd interpret that the other way - there's no publication, this therefore can't be a type, someone used the wrong nature.

added to ID remarks

Perhaps instead of by-request I should just add the original to remarks for everything that gets updated from this. It's no problem to do so.

dustymc on 2 Oct 2019

/remind me to finalize this in 2 weeks

dustymc on 2 Oct 2019

@dustymc set a reminder for Oct 16th 2019

reminders[bot] on 2 Oct 2019

Perhaps instead of by-request I should just add the original to remarks

for everything that gets updated from this. It's no problem to do so.

yes - sounds good

 there's no publication, this therefore can't be a type, someone used

the wrong nature.

Illogical. Nothing prevents people from failing to enter publications for
real types.

& re: revised taxonomy. Just fix the spreadsheet

-D

On Wed, Oct 2, 2019 at 11:25 AM dustymc notifications@github.com wrote:

D - I'd prefer to set them all at once so they don't have an opportunity
to get mixed up with any 'legacy' values.

UPDATE identification SET nature=newthing, confidence=whatever WHERE {anything I can get from existing data - collection, agent, nature, dates, publications, whatever}

is my strong preference.

revised taxonomy.... what argument

I have none - I'm just copying from the spreadsheet!

My concern is there must be specimens with
nature of ID = type specimen that are not linked to publications via a
citation as 'types'

Very possible, and I'd interpret that the other way - there's no
publication, this therefore can't be a type, someone used the wrong nature.

added to ID remarks

Perhaps instead of by-request I should just add the original to remarks
for everything that gets updated from this. It's no problem to do so.

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
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DerekSikes on 2 Oct 2019

Unless someone explicitly directs me otherwise, all updates will include...

AND id_remarks+=Original Nature_of_ID: {oldvalue}

fix the spreadsheet

I don't think that's my call - those values (which have already been implemented) got there by consensus (maybe...). I don't know if someone feels that the current term is better for some reason, or it's just arbitrary. I think @jldunnum had something to say at some point?? @ccicero @campmlc you edited the spreadsheet??

I have no opinion - I think they're saying the same THING, I think it's a straight update (won't require changing confidence), should be easy to update when I figure out how we got here.

dustymc on 2 Oct 2019

Just to reiterate what I wrote previously:

Re: revised taxonomy.... what argument was made to change this back to
taxonomic revision?? I'm sure there's a record of all the discussion on
this but in a nutshell, 'revised taxonomy' is better because the term
'revision' has a specific meaning in taxonomy and not all taxonomic changes
come from taxonomic revisions. Thus it is confusing and misleading to use
'taxonomic revision'. Change the table.

& the history was that this value had been 'taxonomic revision' since
forever... and I argued, and others agreed, to change it to 'revised
taxonomy' so it's baffling to me that people want to change it back & I'd
like to hear what reasoning was behind that?

-Derek

On Wed, Oct 2, 2019 at 11:36 AM dustymc notifications@github.com wrote:

Unless someone explicitly directs me otherwise, all updates will include...

AND id_remarks+=Original Nature_of_ID: {oldvalue}

fix the spreadsheet

I don't think that's my call - those values (which have already been
implemented) got there by consensus (maybe...). I don't know if someone
feels that the current term is better for some reason, or it's just
arbitrary. I think @jldunnum https://github.com/jldunnum had something
to say at some point?? @ccicero https://github.com/ccicero @campmlc
https://github.com/campmlc you edited the spreadsheet??

I have no opinion - I think they're saying the same THING, I think it's a
straight update (won't require changing confidence), should be easy to
update when I figure out how we got here.

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University of Alaska Museum
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Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

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DerekSikes on 2 Oct 2019

I finally found that thread

https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a clue what happened in the meantime.

Unless someone stops me in the very near future I will

change all taxonomic revision to revised taxonomy
allow revised taxonomy for new IDs
remove taxonomic revision from the code table

Bueno?

dustymc on 2 Oct 2019

👍1

Is this why I'm getting this error right now when reiding as Revised taxonomy?
Legacy nature_of_id terms are disallowed; see https://github.com/ArctosDB/arctos/issues/2170
[Macromedia][Oracle JDBC Driver][Oracle]ORA-20001: Legacy nature_of_id terms are disallowed; see https://github.com/ArctosDB/arctos/issues/2170 ORA-06512: at "UAM.TEMP_TR_ID_BIU", line 4 ORA-04088: error during execution of trigger 'UAM.TEMP_TR_ID_BIU'
Error Executing Database Query.
Check the Arctos Handbookhttp://handbook.arctosdb.org/documentation/understanding-errors.html for more information on errors.

Jonathan L. Dunnum Ph.D.
Senior Collection Manager
Division of Mammals, Museum of Southwestern Biology
University of New Mexico
Albuquerque, NM 87131
(505) 277-9262
Fax (505) 277-1351

MSB Mammals website: http://www.msb.unm.edu/mammals/index.html
Facebook: http://www.facebook.com/MSBDivisionofMammals

Shipping Address:
Museum of Southwestern Biology
Division of Mammals
University of New Mexico
CERIA Bldg 83, Room 204
Albuquerque, NM 87131

From: dustymc notifications@github.com
Sent: Wednesday, October 2, 2019 2:45 PM
To: ArctosDB/arctos arctos@noreply.github.com
Cc: Jonathan Dunnum jldunnum@unm.edu; Mention mention@noreply.github.com
Subject: Re: [ArctosDB/arctos] nature of ID (#2170)

I finally found that thread

1093https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a clue what happened in the meantime.

Unless someone stops me in the very near future I will

change all taxonomic revision to revised taxonomy
allow revised taxonomy for new IDs
remove taxonomic revision from the code table

Bueno?

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Reply to this email directly, view it on GitHubhttps://github.com/ArctosDB/arctos/issues/2170?email_source=notifications&email_token=AED2PA6F5VEMBO4CIDWH4N3QMUB7LA5CNFSM4IEIGLOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAGD2FY#issuecomment-537672983, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AED2PA32OON6JQFZK2QEZPLQMUB7LANCNFSM4IEIGLOA.

jldunnum on 2 Oct 2019

Bueno!!

-Derek

On Wed, Oct 2, 2019 at 12:45 PM dustymc notifications@github.com wrote:

I finally found that thread

1093 https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a
clue what happened in the meantime.

Unless someone stops me in the very near future I will

change all taxonomic revision to revised taxonomy

allow revised taxonomy for new IDs

remove taxonomic revision from the code table

Bueno?

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact_us http://www.akentsoc.org/contact.php

DerekSikes on 2 Oct 2019

The rule is flipped - you can use "revised taxonomy" now. I'll update the documentation, flip the values (plus remark), and delete taxonomic revision ~now-ish.

dustymc on 2 Oct 2019

taxonomic revision is no more

dustymc on 2 Oct 2019

awesome

On Wed, Oct 2, 2019 at 1:31 PM dustymc notifications@github.com wrote:

taxonomic revision is no more

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+++++++++++++++++++++++++++++++++++
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact_us http://www.akentsoc.org/contact.php

DerekSikes on 2 Oct 2019

I am getting that same error for Expert as Nature of ID and High confidence.
Can we not change identifications right now?

On Wed, Oct 2, 2019 at 1:45 PM dustymc notifications@github.com wrote:

I finally found that thread

1093 https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a
clue what happened in the meantime.

Unless someone stops me in the very near future I will

change all taxonomic revision to revised taxonomy

allow revised taxonomy for new IDs

remove taxonomic revision from the code table

Bueno?

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Museum of Vertebrate Zoology
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atrox10 on 3 Oct 2019

You can change IDs, but you can't use the terms which are going away very soon. http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID is currently the best source of information.

Let me if I can help update any of your data with a little more finesse than https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537631840

dustymc on 3 Oct 2019

Thanks Dusty!!!

On Wed, Oct 2, 2019 at 5:13 PM dustymc notifications@github.com wrote:

You can change IDs, but you can't use the terms which are going away very
soon.
http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID
is currently the best source of information.

Let me if I can help update any of your data with a little more finesse
than #2170 (comment)
https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537631840

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3101 Valley Life Sciences Building
University of California, Berkeley, CA, USA 94720-3160
[email protected] or [email protected]
510-643-5778
http://mvz.berkeley.edu/

atrox10 on 3 Oct 2019

here's the crosswalk:
ID of kin --> relationship
ID to species group --> unknown
curatorial --> unknown
erroneous citation --> unknown
expert --> FINE FEATURES
field --> COARSE FEATURES
legacy --> unknown - CAN I DO THIS NOW? yes
molecular data--> molecular - CAN I DO THIS NOW? yes
photograph --> COARSE FEATURES?
published referral --> unknown
revised taxonomy --> taxonomic revision - CAN I DO THIS NOW?
student --> unknown
type specimen --> unknown

mkoo on 3 Oct 2019

ID of kin --> relationship
ID to species group --> unknown
curatorial --> FINE FEATURES
erroneous citation --> unknown
expert -->FINE FEATURES
field --> COARSE FEATURES
legacy --> unknown - CAN I DO THIS NOW? yes
molecular data--> molecular - CAN I DO THIS NOW? yes
photograph --> COARSE FEATURES
published referral --> unknown
revised taxonomy --> taxonomic revision - CAN I DO THIS NOW? yes
student --> COARSE FEATURES
type specimen --> FINE FEATURES

campmlc on 3 Oct 2019

select guid_prefix,nature_of_id, count(*) c from collection,cataloged_item,identification where collection.collection_id=cataloged_item.collection_id and cataloged_item.collection_object_id=identification.collection_object_id group by guid_prefix,nature_of_id order by guid_prefix,nature_of_id;


GUID_PREFIX      NATURE_OF_ID                C
-------------------- ------------------------------ ----------
ALMNH:ES         expert                 19
ALMNH:ES         legacy              10351
ALMNH:ES         published referral              3
ALMNH:ES         revised taxonomy                2
ALMNH:ES         type specimen              16
APSU:Herp        legacy               7010
ASNHC:Mamm       field                   1
ASNHC:Mamm       legacy                135
BYU:Herp         field                1281
BYU:Herp         legacy                177
BYU:Herp         photograph                  8
CHAS:Bird        ID to species group             1
CHAS:Bird        expert                139
CHAS:Bird        field                   1
CHAS:Bird        legacy              21858
CHAS:Bird        revised taxonomy                1
CHAS:Bird        student                   230
CHAS:EH          curatorial                  4
CHAS:EH          expert                119
CHAS:EH          legacy                620
CHAS:EH          student                   281
CHAS:Egg         ID of kin                 679
CHAS:Egg         geographic distribution             3
CHAS:Egg         legacy               3337
CHAS:Egg         revised taxonomy                1
CHAS:Egg         student                     1
CHAS:Ento        ID of kin                   1
CHAS:Ento        curatorial                  1
CHAS:Ento        expert                 16
CHAS:Ento        legacy              32137
CHAS:Ento        revised taxonomy               15
CHAS:Ento        student                   564
CHAS:Fish        expert                  1
CHAS:Fish        legacy                 29
CHAS:Herb        expert                 52
CHAS:Herb        field                   9
CHAS:Herb        legacy                 99
CHAS:Herp        expert                  1
CHAS:Herp        legacy                  1
CHAS:Herp        student                     1
CHAS:Inv         curatorial                 34
CHAS:Inv         expert               1971
CHAS:Inv         legacy              25050
CHAS:Inv         published referral              1
CHAS:Inv         revised taxonomy              927
CHAS:Inv         student                    72
CHAS:Inv         type specimen             124
CHAS:Mamm        expert                 37
CHAS:Mamm        field                   2
CHAS:Mamm        geographic distribution             1
CHAS:Mamm        legacy               9912
CHAS:Mamm        revised taxonomy                8
CHAS:Mamm        student                    33
CHAS:Mamm        type specimen              17
CHAS:Teach       ID of kin                   1
CHAS:Teach       expert                 71
CHAS:Teach       field                   1
CHAS:Teach       legacy                954
CHAS:Teach       published referral              1
CHAS:Teach       student                   966
COA:Bird         legacy                878
COA:Egg          legacy                119
COA:Ento         legacy                 37
COA:Herp         legacy                 61
COA:Mamm         legacy                187
DGR:Bird         erroneous citation              1
DGR:Bird         expert                 22
DGR:Bird         field                 351
DGR:Bird         geographic distribution             1
DGR:Bird         legacy               2149
DGR:Bird         molecular data              1
DGR:Bird         revised taxonomy                1
DGR:Bird         type specimen               6
DGR:Ento         legacy                 35
DGR:Mamm         expert                131
DGR:Mamm         field                   2
DGR:Mamm         geographic distribution             3
DGR:Mamm         legacy                664
DGR:Mamm         molecular data             18
DGR:Mamm         revised taxonomy                3
DGR:Mamm         student                     1
DGR:Mamm         type specimen               1
DMNS:Bird        ID of kin                  23
DMNS:Bird        curatorial                 37
DMNS:Bird        erroneous citation             15
DMNS:Bird        expert               1938
DMNS:Bird        field                9106
DMNS:Bird        geographic distribution            42
DMNS:Bird        legacy              42312
DMNS:Bird        molecular data             26
DMNS:Bird        published referral              5
DMNS:Bird        revised taxonomy             3198
DMNS:Bird        student                     5
DMNS:Bird        type specimen              21
DMNS:Egg         field                 182
DMNS:Egg         legacy               6958
DMNS:Egg         published referral              1
DMNS:Egg         revised taxonomy              135
DMNS:Herp        curatorial                  2
DMNS:Herp        expert                 97
DMNS:Herp        field                  13
DMNS:Herp        geographic distribution             7
DMNS:Inv         ID of kin                  12
DMNS:Inv         erroneous citation              2
DMNS:Inv         expert                524
DMNS:Inv         geographic distribution             6
DMNS:Inv         legacy              13118
DMNS:Inv         published referral              3
DMNS:Inv         revised taxonomy             8415
DMNS:Inv         student                 10609
DMNS:Mamm        ID of kin                 185
DMNS:Mamm        ID to species group             5
DMNS:Mamm        curatorial                  4
DMNS:Mamm        expert               3764
DMNS:Mamm        field               15057
DMNS:Mamm        geographic distribution           102
DMNS:Mamm        legacy                544
DMNS:Mamm        molecular data            132
DMNS:Mamm        published referral             21
DMNS:Mamm        revised taxonomy             1108
DMNS:Mamm        student                    29
DMNS:Mamm        type specimen              48
DMNS:Para        expert                771
DMNS:Para        field                  11
DMNS:Para        molecular data              6
DMNS:Para        student                   123
HWML:Para        expert                  4
HWML:Para        legacy              24396
HWML:Para        type specimen            1711
KNWR:Ento        ID of kin                  14
KNWR:Ento        ID to species group             1
KNWR:Ento        erroneous citation              1
KNWR:Ento        expert               3432
KNWR:Ento        field                 223
KNWR:Ento        geographic distribution             3
KNWR:Ento        legacy                 59
KNWR:Ento        molecular data            565
KNWR:Ento        photograph                 59
KNWR:Ento        published referral              9
KNWR:Ento        revised taxonomy              282
KNWR:Ento        student                  8057
KNWR:Ento        type specimen              15
KNWR:Herb        ID of kin                   3
KNWR:Herb        expert               1087
KNWR:Herb        field                  93
KNWR:Herb        legacy                621
KNWR:Herb        molecular data              5
KNWR:Herb        photograph                  2
KNWR:Herb        revised taxonomy               25
KNWR:Herb        student                   721
KNWR:Inv         expert                 25
KNWR:Inv         field                   8
KNWR:Inv         molecular data              6
KNWR:Inv         revised taxonomy                4
KNWR:Inv         student                    26
KNWRObs:Fish         expert                 11
KNWRObs:Herb         field                 830
KWP:Ento         ID to species group           465
KWP:Ento         erroneous citation              2
KWP:Ento         expert              77860
KWP:Ento         geographic distribution           235
KWP:Ento         molecular data              7
KWP:Ento         photograph                259
KWP:Ento         revised taxonomy            34601
KWP:Ento         student                  9520
KWP:Ento         type specimen               1
MLZ:Bird         ID of kin                  21
MLZ:Bird         expert               7046
MLZ:Bird         geographic distribution           245
MLZ:Bird         legacy              62310
MLZ:Bird         published referral           1032
MLZ:Bird         revised taxonomy             2704
MLZ:Bird         type specimen             193
MLZ:Egg          ID of kin                   3
MLZ:Egg          expert                  7
MLZ:Egg          field                   7
MLZ:Egg          legacy                 21
MLZ:Herb         expert                 16
MLZ:Mamm         ID of kin                  10
MLZ:Mamm         expert                  7
MLZ:Mamm         geographic distribution            12
MLZ:Mamm         legacy               2157
MLZ:Mamm         revised taxonomy               25
MSB:Bird         ID of kin                   7
MSB:Bird         expert              13823
MSB:Bird         field                  83
MSB:Bird         legacy              24770
MSB:Bird         molecular data              4
MSB:Bird         revised taxonomy               30
MSB:Bird         student                  6165
MSB:Bird         type specimen              10
MSB:Fish         ID to species group          4648
MSB:Fish         expert              60797
MSB:Fish         field               31708
MSB:Fish         legacy               3122
MSB:Fish         molecular data              1
MSB:Fish         published referral              1
MSB:Fish         revised taxonomy               30
MSB:Fish         student                  3441
MSB:Fish         type specimen               8
MSB:Herp         ID of kin                  20
MSB:Herp         ID to species group             1
MSB:Herp         expert                165
MSB:Herp         field               18873
MSB:Herp         geographic distribution             1
MSB:Herp         legacy              13176
MSB:Herp         revised taxonomy                2
MSB:Herp         student                   102
MSB:Host         ID of kin                  17
MSB:Host         ID to species group             5
MSB:Host         curatorial                  6
MSB:Host         expert                207
MSB:Host         field                3225
MSB:Host         geographic distribution           216
MSB:Host         legacy              22510
MSB:Host         molecular data            247
MSB:Host         published referral              4
MSB:Host         revised taxonomy              753
MSB:Host         student                   168
MSB:Host         type specimen               1
MSB:Mamm         ID of kin                 691
MSB:Mamm         ID to species group             2
MSB:Mamm         curatorial              11815
MSB:Mamm         erroneous citation             45
MSB:Mamm         expert              11063
MSB:Mamm         field               72188
MSB:Mamm         geographic distribution           429
MSB:Mamm         legacy             223114
MSB:Mamm         molecular data           6079
MSB:Mamm         photograph                  7
MSB:Mamm         published referral             15
MSB:Mamm         revised taxonomy            18268
MSB:Mamm         student                 22218
MSB:Mamm         type specimen            4780
MSB:Para         ID of kin                  64
MSB:Para         ID to species group             6
MSB:Para         curatorial                 45
MSB:Para         expert               2494
MSB:Para         field                3492
MSB:Para         legacy              21186
MSB:Para         molecular data            415
MSB:Para         published referral              5
MSB:Para         revised taxonomy               13
MSB:Para         student                  2438
MSB:Para         type specimen              68
MSBObs:Mamm      ID of kin                   3
MVZ:Bird         ID of kin                   4
MVZ:Bird         ID to species group          4019
MVZ:Bird         coarse features                 9
MVZ:Bird         expert               1327
MVZ:Bird         field                3807
MVZ:Bird         geographic distribution         11466
MVZ:Bird         legacy             180916
MVZ:Bird         molecular data             56
MVZ:Bird         published referral             11
MVZ:Bird         revised taxonomy            54185
MVZ:Bird         student                     2
MVZ:Bird         type specimen             482
MVZ:Egg          ID of kin                   1
MVZ:Egg          ID to species group           247
MVZ:Egg          expert                 24
MVZ:Egg          field                 407
MVZ:Egg          geographic distribution          1010
MVZ:Egg          legacy              14386
MVZ:Egg          published referral             10
MVZ:Egg          revised taxonomy             3315
MVZ:Fish         field                   1
MVZ:Herp         ID of kin                  11
MVZ:Herp         ID to species group           182
MVZ:Herp         curatorial                  1
MVZ:Herp         erroneous citation              5
MVZ:Herp         expert              15964
MVZ:Herp         field               51074
MVZ:Herp         fine features               4
MVZ:Herp         geographic distribution          3045
MVZ:Herp         legacy             228836
MVZ:Herp         molecular data            227
MVZ:Herp         photograph                  4
MVZ:Herp         published referral            699
MVZ:Herp         revised taxonomy            35319
MVZ:Herp         student                    18
MVZ:Herp         type specimen            4389
MVZ:Hild         expert                  3
MVZ:Hild         field                  72
MVZ:Hild         legacy                585
MVZ:Hild         revised taxonomy                6
MVZ:Mamm         ID of kin                1466
MVZ:Mamm         ID to species group             1
MVZ:Mamm         curatorial                  3
MVZ:Mamm         erroneous citation              1
MVZ:Mamm         expert              40893
MVZ:Mamm         field               15624
MVZ:Mamm         geographic distribution          3713
MVZ:Mamm         legacy             193130
MVZ:Mamm         molecular data            530
MVZ:Mamm         published referral             89
MVZ:Mamm         revised taxonomy            20240
MVZ:Mamm         student                   858
MVZ:Mamm         type specimen            1844
MVZObs:Bird      ID to species group             3
MVZObs:Bird      expert                  3
MVZObs:Bird      field                4621
MVZObs:Bird      geographic distribution          1565
MVZObs:Bird      legacy                238
MVZObs:Bird      revised taxonomy              524
MVZObs:Herp      expert                  3
MVZObs:Herp      field                  19
MVZObs:Herp      photograph                  6
MVZObs:Herp      type specimen               1
MVZObs:Mamm      field                 101
NBSB:Bird        field                 321
NMU:Bird         ID of kin                   3
NMU:Bird         field                 308
NMU:Bird         legacy                  9
NMU:Mamm         ID of kin                  58
NMU:Mamm         expert                 70
NMU:Mamm         field                1203
NMU:Mamm         geographic distribution            95
NMU:Mamm         legacy               1026
NMU:Mamm         molecular data             87
NMU:Mamm         student                     2
NMU:Para         field                   7
OWU:Bird         curatorial                  2
OWU:Bird         student                    26
OWU:ES           curatorial                  3
OWU:ES           expert                 52
OWU:ES           field                   4
OWU:ES           legacy                297
OWU:ES           revised taxonomy               25
OWU:Fish         curatorial                 16
OWU:Fish         field                   1
OWU:Fish         student                     5
OWU:Mamm         ID of kin                   7
OWU:Mamm         curatorial                  7
OWU:Mamm         field                   1
OWU:Mamm         legacy                153
OWU:Mamm         student                     2
OWU:Para         curatorial                  2
OWU:Para         expert                  3
OWU:Rept         curatorial                  7
OWU:Rept         field                  81
OWU:Rept         legacy                137
UAM:Alg          legacy               4639
UAM:Arc          ID of kin               22859
UAM:Arc          expert               8502
UAM:Arc          field                 301
UAM:Arc          legacy             615096
UAM:Arc          student                   558
UAM:Art          expert                422
UAM:Art          legacy               3873
UAM:Bird         expert               1135
UAM:Bird         field               29489
UAM:Bird         legacy               7055
UAM:Bird         revised taxonomy                2
UAM:Bird         type specimen             156
UAM:EH           ID of kin                 890
UAM:EH           curatorial                 85
UAM:EH           expert                144
UAM:EH           field                   1
UAM:EH           legacy              14653
UAM:EH           photograph                  1
UAM:EH           student                   175
UAM:ES           ID of kin                  39
UAM:ES           erroneous citation              1
UAM:ES           expert              27465
UAM:ES           field               20062
UAM:ES           molecular data             14
UAM:ES           photograph                  1
UAM:ES           published referral              2
UAM:ES           revised taxonomy              292
UAM:ES           student                  7916
UAM:ES           type specimen               7
UAM:Ento         ID of kin                 447
UAM:Ento         ID to species group             1
UAM:Ento         coarse features                13
UAM:Ento         curatorial                753
UAM:Ento         erroneous citation             45
UAM:Ento         expert             279626
UAM:Ento         field                3018
UAM:Ento         geographic distribution           783
UAM:Ento         legacy              10861
UAM:Ento         molecular                   2
UAM:Ento         molecular data           1241
UAM:Ento         photograph                 47
UAM:Ento         published referral             38
UAM:Ento         revised taxonomy            21669
UAM:Ento         student                236131
UAM:Ento         type specimen             103
UAM:Env          student                   334
UAM:Fish         ID of kin                  25
UAM:Fish         expert               1980
UAM:Fish         field                1422
UAM:Fish         geographic distribution             4
UAM:Fish         legacy               6841
UAM:Fish         molecular data             20
UAM:Fish         revised taxonomy              472
UAM:Fish         student                    40
UAM:Fish         type specimen               3
UAM:Herb         ID of kin                 146
UAM:Herb         curatorial                  1
UAM:Herb         erroneous citation             10
UAM:Herb         expert              15290
UAM:Herb         field                2173
UAM:Herb         geographic distribution             3
UAM:Herb         legacy             201740
UAM:Herb         molecular data             24
UAM:Herb         revised taxonomy             2267
UAM:Herb         student                  9338
UAM:Herb         type specimen             515
UAM:Herp         ID of kin                   1
UAM:Herp         expert                 21
UAM:Herp         field                 383
UAM:Herp         geographic distribution             2
UAM:Herp         legacy                 35
UAM:Herp         molecular data              2
UAM:Herp         revised taxonomy              183
UAM:Herp         student                    44
UAM:Herp         type specimen               2
UAM:Inv          ID of kin                   9
UAM:Inv          expert                 89
UAM:Inv          field                 306
UAM:Inv          geographic distribution             4
UAM:Inv          legacy              19832
UAM:Inv          revised taxonomy                8
UAM:Inv          student                    56
UAM:Inv          type specimen              21
UAM:Mamm         ID of kin                 396
UAM:Mamm         curatorial                219
UAM:Mamm         erroneous citation              1
UAM:Mamm         expert               2867
UAM:Mamm         field               46898
UAM:Mamm         geographic distribution           655
UAM:Mamm         legacy              62850
UAM:Mamm         molecular data            654
UAM:Mamm         published referral              3
UAM:Mamm         revised taxonomy            20784
UAM:Mamm         student                 29046
UAM:Mamm         type specimen            6710
UAMObs:Bird      field                 164
UAMObs:Ento      ID of kin                  12
UAMObs:Ento      ID to species group             1
UAMObs:Ento      erroneous citation             22
UAMObs:Ento      expert              14216
UAMObs:Ento      field                  14
UAMObs:Ento      geographic distribution           129
UAMObs:Ento      legacy              18638
UAMObs:Ento      molecular                   1
UAMObs:Ento      molecular data           3168
UAMObs:Ento      photograph                 30
UAMObs:Ento      published referral           1981
UAMObs:Ento      revised taxonomy             1982
UAMObs:Ento      student                  1768
UAMObs:Ento      type specimen            1353
UAMObs:Fish      field                   6
UAMObs:Fish      photograph                  7
UAMObs:Mamm      ID of kin                   1
UAMObs:Mamm      curatorial                  1
UAMObs:Mamm      field                 212
UAMObs:Mamm      photograph                 20
UAMObs:Mamm      student                    20
UAMObs:Mamm      type specimen               7
UAMb:Herb        expert              11160
UAMb:Herb        field                   9
UAMb:Herb        geographic distribution             1
UAMb:Herb        legacy              52444
UAMb:Herb        photograph                  1
UAMb:Herb        student                   208
UCM:Bird         ID of kin                   1
UCM:Bird         curatorial                  3
UCM:Bird         erroneous citation              1
UCM:Bird         expert               1073
UCM:Bird         field                   2
UCM:Bird         legacy              11122
UCM:Bird         revised taxonomy               35
UCM:Bird         student                     1
UCM:Bird         type specimen               8
UCM:Egg          ID of kin                   1
UCM:Egg          expert                760
UCM:Egg          legacy               2436
UCM:Egg          revised taxonomy               18
UCM:Egg          student                   153
UCM:Fish         ID of kin                   5
UCM:Fish         ID to species group             1
UCM:Fish         expert                294
UCM:Fish         field                   1
UCM:Fish         legacy               2107
UCM:Fish         revised taxonomy               23
UCM:Fish         student                    11
UCM:Fish         type specimen              25
UCM:Herp         curatorial                 80
UCM:Herp         expert               3349
UCM:Herp         field                   1
UCM:Herp         geographic distribution           413
UCM:Herp         legacy              63160
UCM:Herp         photograph                  1
UCM:Herp         published referral             15
UCM:Herp         revised taxonomy            25751
UCM:Herp         student                     1
UCM:Herp         type specimen             510
UCM:Mamm         expert               1476
UCM:Mamm         field                  13
UCM:Mamm         geographic distribution            11
UCM:Mamm         legacy              19077
UCM:Mamm         molecular data            106
UCM:Mamm         published referral              3
UCM:Mamm         revised taxonomy              223
UCM:Mamm         student                    11
UCM:Mamm         type specimen              28
UCM:Obs          expert                 26
UCM:Obs          field                 205
UCM:Obs          photograph                 20
UCM:Obs          revised taxonomy               36
UCSC:Bird        legacy                175
UCSC:Herp        legacy                  1
UCSC:Mamm        field                 173
UCSC:Mamm        legacy                 24
UMNH:Bird        curatorial                 46
UMNH:Bird        expert                  5
UMNH:Bird        field                  41
UMNH:Bird        legacy              20741
UMNH:Bird        revised taxonomy                3
UMNH:Herp        field                   4
UMNH:Herp        legacy              22431
UMNH:Mamm        ID of kin                  52
UMNH:Mamm        curatorial                354
UMNH:Mamm        expert                 71
UMNH:Mamm        field                3055
UMNH:Mamm        geographic distribution            35
UMNH:Mamm        legacy              40169
UMNH:Mamm        published referral              1
UMNH:Mamm        revised taxonomy              133
UMNH:Mamm        student                     6
UMNH:Mamm        type specimen              18
UMZM:Bird        legacy               6161
UMZM:Mamm        legacy              15830
UNM:ES           ID of kin                   2
UNM:ES           expert                603
UNM:ES           legacy                205
UNM:ES           revised taxonomy               72
UNM:ES           student                   768
UNR:Bird         field                 198
UNR:Fish         ID of kin                  32
UNR:Fish         expert                 66
UNR:Fish         field                3028
UNR:Fish         legacy                205
UNR:Fish         student                   484
UNR:Herp         ID of kin                   3
UNR:Herp         expert                  7
UNR:Herp         field                3589
UNR:Herp         student                     1
UNR:Mamm         ID of kin                   1
UNR:Mamm         field                2016
USNPC:Para       expert                809
USNPC:Para       legacy                  1
USNPC:Para       type specimen               1
UTEP:Arc         expert                451
UTEP:Bird        expert                631
UTEP:Bird        legacy               2426
UTEP:Bird        student                    22
UTEP:ES          ID of kin                 604
UTEP:ES          erroneous citation              3
UTEP:ES          expert              23715
UTEP:ES          legacy                276
UTEP:ES          molecular data              1
UTEP:ES          revised taxonomy              138
UTEP:ES          student                    35
UTEP:ES          type specimen              18
UTEP:Ento        curatorial                  5
UTEP:Ento        expert                530
UTEP:Ento        legacy               7828
UTEP:Ento        student                    32
UTEP:Ento        type specimen              40
UTEP:Fish        expert                 93
UTEP:Fish        field                   4
UTEP:Fish        legacy                  1
UTEP:Fish        student                   147
UTEP:Herb        curatorial                 44
UTEP:Herb        erroneous citation              1
UTEP:Herb        expert              49407
UTEP:Herb        field                 104
UTEP:Herb        legacy              34787
UTEP:Herb        molecular data             47
UTEP:Herb        student                    36
UTEP:Herb        type specimen              15
UTEP:Herp        ID of kin                   4
UTEP:Herp        curatorial                613
UTEP:Herp        expert              10223
UTEP:Herp        field                 113
UTEP:Herp        geographic distribution            37
UTEP:Herp        legacy              11595
UTEP:Herp        molecular data            145
UTEP:Herp        revised taxonomy               24
UTEP:Herp        student                    11
UTEP:Herp        type specimen             336
UTEP:HerpOS      expert                572
UTEP:HerpOS      geographic distribution             2
UTEP:HerpOS      legacy               1166
UTEP:HerpOS      type specimen               1
UTEP:Inv         expert              10207
UTEP:Inv         legacy               1697
UTEP:Inv         type specimen              21
UTEP:Mamm        ID of kin                  20
UTEP:Mamm        expert               8517
UTEP:Mamm        geographic distribution            39
UTEP:Mamm        revised taxonomy                2
UTEP:Teach       expert                 62
UTEP:Teach       field                   1
UTEP:Teach       legacy                180
UTEP:Teach       revised taxonomy                2
UTEP:Teach       student                     2
UTEP:Zoo         expert                 17
UTEP:Zoo         student                   107
UTEP:Zoo         type specimen              27
UTEPObs:Ento         expert                  2
UTEPObs:Herp         ID of kin                   1
UTEPObs:Herp         expert                 75
UTEPObs:Herp         field                  20
UTEPObs:Herp         legacy                 73
UTEPObs:Herp         photograph                 22
UWBM:Herp        ID of kin                 897
UWBM:Herp        expert                568
UWBM:Herp        field                1141
UWBM:Herp        geographic distribution             2
UWBM:Herp        legacy               7754
UWBM:Herp        revised taxonomy               89
UWBM:Herp        student                   164
UWBM:Herp        type specimen               2
UWBM:Mamm        ID of kin                   3
UWBM:Mamm        ID to species group             2
UWBM:Mamm        expert                 14
UWBM:Mamm        field                   4
UWBM:Mamm        legacy              55660
UWYMV:Bird       ID of kin                   1
UWYMV:Bird       curatorial                 12
UWYMV:Bird       expert               2217
UWYMV:Bird       field                  52
UWYMV:Bird       geographic distribution           122
UWYMV:Bird       legacy                  3
UWYMV:Bird       student                    30
UWYMV:Egg        geographic distribution             1
UWYMV:Egg        student                     1
UWYMV:Fish       expert                539
UWYMV:Herp       curatorial                  2
UWYMV:Herp       expert                346
UWYMV:Herp       field                   1
UWYMV:Herp       legacy                  3
UWYMV:Mamm       curatorial                 19
UWYMV:Mamm       expert                  1
UWYMV:Mamm       field                   4
UWYMV:Mamm       geographic distribution          1112
UWYMV:Mamm       legacy               5222
WNMU:Bird        legacy               1339
WNMU:Fish        expert                 55
WNMU:Fish        legacy                324
WNMU:Mamm        expert                 16
WNMU:Mamm        legacy               6542
WNMU:Mamm        revised taxonomy              332

dustymc on 3 Oct 2019

Find your types in USAGE!

Dusty will implement the migration outlined in Mariel's last comment in two weeks-- complain before then or make changes accordingly.

mkoo on 3 Oct 2019

Seems Mariel didn't catch the discussion on this:

revised taxonomy --> taxonomic revision - CAN I DO THIS NOW? yes

The conclusions was NO, this is not going to happen. All 'taxonomic
revision' will become 'revised taxonomy', not the other way around.

-Derek

On Thu, Oct 3, 2019 at 11:07 AM Michelle Koo notifications@github.com
wrote:

Find your types in USAGE!

Dusty will implement the migration outlined in Mariel's last comment in
two weeks-- complain before then or make changes accordingly.

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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

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DerekSikes on 3 Oct 2019

Revised taxonomy is done.

Current values will be preserved in remarks.

Relevant code tables are https://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID and https://arctos.database.museum/info/ctDocumentation.cfm?table=CTIDENTIFICATION_CONFIDENCE

These will happen ~today unless someone stops me:

legacy --> unknown
molecular data--> molecular

These will happen for anything that hasn't been handled about Oct 16th 2019. PLEASE comment here ASAP if you'd like a different migration path (eg, one that does something with 'confidence') for some or all of your collection.

ID of kin --> relationship
ID to species group --> unknown
curatorial --> FINE FEATURES
erroneous citation --> unknown
expert -->FINE FEATURES
field --> COARSE FEATURES
photograph --> COARSE FEATURES
published referral --> unknown
student --> COARSE FEATURES
type specimen --> FINE FEATURES

dustymc on 3 Oct 2019

Good.

For UAM:Ento, UAMObs:Ento, KWP:Ento, KNWR:Ento, and KNWR:Inv

I would like confidence set to 'high' for any identifications with nature
of ID = expert
&
I would like confidence set to 'medium' for any identifications with nature
of ID = student

I am not sure about this migration:

expert -->FINE FEATURES
student --> COARSE FEATURES

I think this is incorrect - lots of student IDs are based on 'fine
features'; similar problem with photograph... plenty of IDs based on photos
are of fine features (eg SEM or any photos taken through microscopes...)

I'm a little worried that we'll be forced to make distinctions between FINE
& COARSE that are over-precise and subjective. It would be good to have a
3rd option "PHENOTYPE" or "MORPHOLOGY" or perhaps "EXTERNAL FEATURES" for
cases where we don't know if the ID was based on FINE or COARSE features.
Sorry if this sets us back a bit.

-Derek

On Thu, Oct 3, 2019 at 11:54 AM dustymc notifications@github.com wrote:

Revised taxonomy is done.

Current values will be preserved in remarks.

Relevant code tables are
https://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID
and
https://arctos.database.museum/info/ctDocumentation.cfm?table=CTIDENTIFICATION_CONFIDENCE

These will happen ~today unless someone stops me:

legacy --> unknown

molecular data--> molecular

These will happen for anything that hasn't been handled about Oct 16th

PLEASE comment here ASAP if you'd like a different migration path
(eg, one that does something with 'confidence') for some or all of your
collection.

ID of kin --> relationship

ID to species group --> unknown

curatorial --> FINE FEATURES

erroneous citation --> unknown

expert -->FINE FEATURES

field --> COARSE FEATURES

photograph --> COARSE FEATURES

published referral --> unknown

student --> COARSE FEATURES

type specimen --> FINE FEATURES

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+++++++++++++++++++++++++++++++++++
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact_us http://www.akentsoc.org/contact.php

DerekSikes on 3 Oct 2019

I don't disagree; my "morphology" proposal died ^^ way up there ^^ somewhere.

I'm not sure anything like SEM is required to get at "fine" - think keying out blue vs. fin whale skulls.

I don't like "external" - think "this adult bear femur is obviously a grizzly because it looks like one."

Given the existing overlap, another hopefully-temporary morphology-or-whatever(==we don't know what "fine" and "course" mean so we don't know if this should be "fine" or "course") option would not bother me too much, particularly if it lets us proceed.

Alternatively, I still like "unknown" (https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537631840) for these. I suppose it's a matter of how much we don't know before we admit we don't know....

dustymc on 3 Oct 2019

What about "external phenoype" (looks like moose") vs "anatomy" (internal morphology/structure) vs "microscopy"?

ccicero on 4 Oct 2019

external phenoype

I think I like it.

"anatomy" vs "microscopy"

Are these different or just taxon-specific things? Folks who look at grasshopper genitalia under a microscope are doing about the same things (probably, I think) as those who look at large mammal femurs, it's just that the latter don't require magnification.

I think there's a place for "took 600 detailed measurements of this sea lion skull from the CT scan" - maybe "microscopy" works for that and we just need to be careful in the definition?

dustymc on 4 Oct 2019

I think morphology fits all these. If I look at mouse teeth, is that
external or internal?

On Thu, Oct 3, 2019 at 4:54 PM dustymc notifications@github.com wrote:

external phenoype

I think I like it.

"anatomy" vs "microscopy"

Are these different or just taxon-specific things? Folks who look at
grasshopper genitalia under a microscope are doing about the same things
(probably, I think) as those who look at large mammal femurs, it's just
that the latter don't require magnification.

I think there's a place for "took 600 detailed measurements of this sea
lion skull from the CT scan" - maybe "microscopy" works for that and we
just need to be careful in the definition?

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campmlc on 4 Oct 2019

I think external phenotype is better for a general 'looks like a moose' or "looks like a certain subspecies of a bird" scenario. Morphology doesn't really cover looking at plumage characteristics, for example. Definition: "Identification based on a coarse examination of external features including size, shape, and color."

I think anatomy would cover things like looking at teeth, bones, appendages, etc. - whether under a scope or not. Definition: "Identification based on a detailed look at structure such as teeth, bones, appendages, etc. whether under a microscope or not."

I was trying to figure out another word for 'microscopy' that would cover things like CT scans or something that requires specialized equipment. "Microscopy" probably isn't the best term. What about "Advanced Imaging" - Definition: "Identification based on advanced imaging technology, including CT scanning, Scanning Electron Microscopy (SEM), etc."

So these three terms would cover progressively more advanced, detailed examination of features for identification.

ccicero on 4 Oct 2019

I'm still not quite seeing the split between anatomy and "microscopy." https://arctos.database.museum/guid/UAM:Mamm:11507 was done with calipers. There's a grant pending to do the same(ish) thing with CT/digital measuring. I don't think the results will be fundamentally different, so I don't think the equipment is a useful split.

Does "detailed measurements" (however we say it) work for the last category? So LOOKING (and maybe making some casual measurements), whether it's at a blue whale or a virus, is "anatomy," but carefully measuring characteristics is something else.

I think that works for more than morphology as well - quantitative colors, maybe some of the stuff that happens around bat detectors, testing artwork for caesium-137 (maybe that's molecular??), etc.

dustymc on 4 Oct 2019

What about "general phenotype" for field or "casual" IDs (could include casual measurements, scale counts). I like the term phenotype because most field ids are based on that.

I agree we need something for more careful analysis, could be scans or quantitative color analysis etc. Something more advanced that contrasts with "general"

ccicero on 4 Oct 2019

I like the wording of General Phenotype.
But since we are really just trying to get back to how we ID things in the
field (which are possibly by an expert but checked quickly with only some
or no reference material available), why can't we keep "field" as one
possibility?
"general phenotype" can be another.
It conveys a lot on how the animal or plant, etc was identified. Whereas
all the others our more specific about tools used, etc.

On Fri, Oct 4, 2019 at 9:28 AM Carla Cicero notifications@github.com
wrote:

What about "general phenotype" for field or "casual" IDs (could include
casual measurements, scale counts). I like the term phenotype because most
field ids are based on that.

I agree we need something for more careful analysis, could be scans or
quantitative color analysis etc. Something more advanced that contrasts
with "general"

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atrox10 on 4 Oct 2019

Don't we have to consider cultural objects? Maybe this is why we settled on
'features' initially?

I think features is fine I just feel we need an alternative for when we
don't know if the examination was of coarse or fine features...

maybe 'feature examination' ? pretty vague but works & is better than
'unknown'

-Derek

On Fri, Oct 4, 2019 at 8:28 AM Carla Cicero notifications@github.com
wrote:

What about "general phenotype" for field or "casual" IDs (could include
casual measurements, scale counts). I like the term phenotype because most
field ids are based on that.

I agree we need something for more careful analysis, could be scans or
quantitative color analysis etc. Something more advanced that contrasts
with "general"

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DerekSikes on 4 Oct 2019

I don't think "phenotype" works for all of Arctos. "This looks like a Clovis point" and "the 800 measurements that fell out of the CT analysis support this being a Clovis point" should work alongside biological material.

The objections yesterday arose around the split between "general" and "detailed" (whatever we ultimately call them). It would be good if the terms themselves included/excluded "sorta-detailed" things like scale count, but that can probably be in the definition as well.

dustymc on 4 Oct 2019

field

I think that would fail to support what we're trying to do here. If we can get at HOW an ID was made, then people can search for cryptospecies (eg, things that look the same under some technique) and such. Saying where it was made (and I think "field" would be used for that, however it's defined) can't do that; people do drag microscopes to the field.

"Expertness" should be derived from the identifier's agent record and the new "confidence" field.

dustymc on 4 Oct 2019

'feature examination' ? pretty vague but works & is better than 'unknown'

I think this is confounding some stuff.

We should have clear terminology going forward; if you {whatever} then you need to use term {something}.
We need a migration path. I don't think there's a universal landing spot for the stuff currently in nature of ID (that's the problem we're trying to fix). Expert, student, curatorial, etc., all could have come from any technique. From here, at the scope of Arctos, I have absolutely no way to say more; I just don't know, and that's what "unknown" says. You may know more - 'experts' in your collection always use 'feature examination' or something. If you have that (or are willing to guess - the existing data will be preserved in remarks, I don't think this has to be perfect) PLEASE let me know so I can write custom migration scripts and move those records now, so they're not caught up in the default/fallback migration.

dustymc on 4 Oct 2019

I don't think "phenotype" works for all of Arctos.

Please no biologically-specific terms. "Features" was a much more inclusive term for all collections held in Arctos.

AJLinn on 4 Oct 2019

I think we need a 'general features' term, and it should be easy to adjust the name as long as we don't significantly alter the concept.
I think we need a 'fine features' term, and it should be easy to adjust the name as long as we don't significantly alter the concept.
Do we also need a "features" term that encompasses both of the above? I think this is the current blocker.

dustymc on 4 Oct 2019

I second the request for a term that is inclusive of non-biological
collections.

On Fri, Oct 4, 2019 at 9:29 AM dustymc notifications@github.com wrote:

>

I think we need a 'general features' term, and it should be easy to
adjust the name as long as we don't significantly alter the concept.

I think we need a 'fine features' term, and it should be easy to
adjust the name as long as we don't significantly alter the concept.

Do we also need a "features" term that encompasses both of the
above? I think this is the current blocker.

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marecaguthrie on 4 Oct 2019

Do we also need a "features" term that encompasses both of the above? I
think this is the current blocker.

yes - and for migration it's much safer and more appropriate to use this
'features' without specifying fine or coarse for nature of ID = expert and
student, even for 'field' because all such IDs sometimes use coarse and
sometimes use fine features. We cannot assume that experts use fine and
students use coarse. Experts can look at a moose femur in the woods and
know it's moose without a microscope, students can use microscopes etc.

-Derek

On Fri, Oct 4, 2019 at 9:29 AM dustymc notifications@github.com wrote:

>

I think we need a 'general features' term, and it should be easy to
adjust the name as long as we don't significantly alter the concept.

I think we need a 'fine features' term, and it should be easy to
adjust the name as long as we don't significantly alter the concept.

Do we also need a "features" term that encompasses both of the
above? I think this is the current blocker.

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DerekSikes on 4 Oct 2019

Done.

features - Identification based on examination of diagnostic traits that may include qualitiative assessment of morphology, coloration, structure, etc. Examination of features may be direct (specimen) or indirect (e.g., photograph). This value encompasses "fine features" and "coarse features" and should not be used if more specific information is available.

dustymc on 4 Oct 2019

But I can't use 'features' for new IDs - getting that legacy terms error

On Fri, Oct 4, 2019 at 10:14 AM dustymc notifications@github.com wrote:

Done.

features - Identification based on examination of diagnostic traits that
may include qualitiative assessment of morphology, coloration, structure,
etc. Examination of features may be direct (specimen) or indirect (e.g.,
photograph). This value encompasses "fine features" and "coarse features"
and should not be used if more specific information is available.

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DerekSikes on 4 Oct 2019

You can now - one of the many reasons I don't want to let this hang out in never-never land for too long....

dustymc on 4 Oct 2019

So are we down to just one term of "features"?

I thin it will be confusing to have three "features" term - general, fine, no modifier. I am fine with just the one term, to distinguish between that and molecular, audio-visual, relationships, etc

Dusty, can you provide the most current list and migration path?

ccicero on 4 Oct 2019

No, we are up to three.

At least in theory I think we need more than one, but if there's no compelling immediate need I'm happy enough to drop 'fine' and 'course' and deal with that when someone needs it.

I don't think this changes anything about my migration path; there's still nothing about eg, 'expert' that might lead me to 'features' so I see no alternative but to map it to 'unknown.' I continue hoping that collections WILL have that information (or be willing to make educated guesses at it) and will direct me to better pathways before I have to fall back to shoving most everything into 'unknown' (and remarks). I think ID of kin --> relationship is currently the only unambiguous not-unknown path I have.

dustymc on 4 Oct 2019

no, there are 3 terms:

fine features
coarse features
features

the last one is only to be used when one can't be sure on which of the
first two to apply

On Fri, Oct 4, 2019 at 11:06 AM Carla Cicero notifications@github.com
wrote:

So are we down to just one term of "features"?

I thin it will be confusing to have three "features" term - general, fine,
no modifier. I am fine with just the one term, to distinguish between that
and molecular, audio-visual, relationships, etc

Dusty, can you provide the most current list and migration path?

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DerekSikes on 4 Oct 2019

In thinking more about this, what are we trying to accomplish by having three terms for essentially the same type of ID, just with more or less detail? I think that's going to cause confusion. That would be like breaking 'molecular' into different types of analysis (genomics, mtDNA sequences, etc.).

Can't we just have one term for 'features' - someone ID'd it based on external or internal features such as size, shape, color, etc. - and then deal with the details if someone wants in other fields, either ID_Remarks or attributes (measurements, color...) plus our new confidence score?

I think we need to step back a bit and ask what our goals are.

ccicero on 5 Oct 2019

accomplish

In theory, I'm thinking

"someone looked at large-scale morphology, this could very well be a morphological cryptospecies, we might detect that with more detailed morphology."
same thing, but 'detailed morphology' --> genetics-or-something

I'm not sure anyone's ever tried to find specimens in that way (they've certainly failed if they tried) so as long as we're not losing data - and I don't think it's currently there to lose - I am fine with adding that when/if we have the actual need.

https://arctos.database.museum/guid/UAM:Mamm:11507 is an example of a "fine features" specimen, but that's not apparent from the current data, and I don't think we'd lose anything by merging it into 'features.' (And it's not so much "fine features' as 'precise measurements.')

dustymc on 7 Oct 2019

Right. Also, looking at fine features is different than basing an ID on that. You can base the ID on its features, but then examine fine features and add those as other types of data such as attributes, media, etc. For identification, I think the important thing is to distinguish whether it was based on features, molecular data, audio-visual, distribution, etc.

ccicero on 7 Oct 2019

Not to throw a new wrench into the works... but may the most important
thing we're trying to capture is:
FIRST, the confidence or some measure of that (preliminary id vs
verified)-- this is really the Nature of Id (quality)
SECOND, the method of how that id was made (fine, coarse, or external
(trying to get at something less biological than phenotype) vs molecular),
etc etc (more quantitative although the method may be based on quality or
gestalt or whatever, for ex., if Patton says he "feels" it's a particular
subspecies of gopher I'd have more confidence than if anyone else did)

If we think of it that way, then maybe we dont have to parse/ dissect /
enumerate terms like "Fine" which just is giving me hives

On Mon, Oct 7, 2019 at 8:38 AM Carla Cicero notifications@github.com
wrote:

Right. Also, looking at fine features is different than basing an ID on
that. You can base the ID on its features, but then examine fine features
and add those as other types of data such as attributes, media, etc. For
identification, I think the important thing is to distinguish whether it
was based on features, molecular data, audio-visual, distribution, etc.

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mkoo on 7 Oct 2019

@mkoo I think those things are all closely related, and that's part of what we're doing here.

Patton thinks it looks like a gopher based on some technique (nature_of_id) he's familiar with
Patton thinks it looks like a gopher based on some technique he's familiar with, but notes that the diagnostic features are mangled
Patton thinks it looks like a gopher based on some technique that he's never used before
Some student who came to know gophers exists about 5 minutes ago does the same things....

I think you need all of that to understand an identification. "Patton is an expert (and he may or may not have been working in familiar territory or with identifiable specimens)" doesn't say much.

dustymc on 7 Oct 2019

yes, what I'm saying is:
nature of id= validated or high confidence or verified or whatever term we
like
method of id= Patton ran allozymes.

user= feels good that it's gopher X

or
nature of id= preliminary or low confidence or unvalidated
method of id= some student looked at external morphology while wrangling
out of its trap (i.e., "field")

user= hmm, (data) buyer beware

On Mon, Oct 7, 2019 at 9:00 AM dustymc notifications@github.com wrote:

@mkoo https://github.com/mkoo I think those things are all closely
related, and that's part of what we're doing here.

Patton thinks it looks like a gopher based on some technique
(nature_of_id) he's familiar with

Patton thinks it looks like a gopher based on some technique he's
familiar with, but notes that the diagnostic features are mangled

Patton thinks it looks like a gopher based on some technique that
he's never used before

Some student who came to know gophers exists about 5 minutes ago
does the same things....

I think you need all of that to understand an identification. "Patton is
an expert (and he may or may not have been working in familiar territory or
with identifiable specimens)" doesn't say much.

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mkoo on 7 Oct 2019

That's what we're doing, but not with that vocabulary.

method ==> nature_of_id
validated or high confidence or verified or whatever term we like ==> identification_confidence

dustymc on 7 Oct 2019

yea I'm saying flip that! we see the nature of id first and it's a quality
measurement not the method that's primary. Currently, we are trying to
implicitly derive the quality from the method which is not efficient and
where we get lost in the fine vs coarse dissections.

On Mon, Oct 7, 2019 at 9:36 AM dustymc notifications@github.com wrote:

That's what we're doing, but not with that vocabulary.

method ==> nature_of_id
validated or high confidence or verified or whatever term we like ==>
identification_confidence

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mkoo on 7 Oct 2019

I don't think that's a blocker - we can flip labels whenever we want.
Treating an explicitly-subjective NULLable field that many collections have said they won't use as "primary" doesn't make sense to me.

dustymc on 7 Oct 2019

No, we would alter the crosswalk so it's not nullable... I'm talking about
a conceptual "flip" and moving our model of nature of id so that it better
captures confidence quality. Because that is implicitly what we are trying
to do with things like nature of id="field" vs "expert"

perhaps better to have as a priority conversation topic as I feel that
others will have opinions on this who are not part of this thread.

On Mon, Oct 7, 2019 at 9:49 AM dustymc notifications@github.com wrote:

>

I don't think that's a blocker - we can flip labels whenever we
want.

Treating an explicitly-subjective NULLable field that many
collections have said they won't use as "primary" doesn't make sense to me.

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mkoo on 7 Oct 2019

I feel we're going backwards here.

We added the new field 'ID confidence' which clearly captures what was
mixed with 'id method' in 'nature of ID' - maybe we need to change the name
of the field from 'nature of id' to 'id method' to make it even more
explicit:

ID confidence
ID method

-Derek

On Mon, Oct 7, 2019 at 8:56 AM Michelle Koo notifications@github.com
wrote:

No, we would alter the crosswalk so it's not nullable... I'm talking about
a conceptual "flip" and moving our model of nature of id so that it better
captures confidence quality. Because that is implicitly what we are trying
to do with things like nature of id="field" vs "expert"

perhaps better to have as a priority conversation topic as I feel that
others will have opinions on this who are not part of this thread.

On Mon, Oct 7, 2019 at 9:49 AM dustymc notifications@github.com wrote:

>

I don't think that's a blocker - we can flip labels whenever we
want.

Treating an explicitly-subjective NULLable field that many
collections have said they won't use as "primary" doesn't make sense to
me.

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DerekSikes on 7 Oct 2019

backwards

Certainly somewhere we've been before.

method

That's just labels - we can go there without getting stuck here.

dustymc on 7 Oct 2019

so maybe ID confidence is the new nature of id-- put that at top
ID method is a new field with the nature of id values with all the
variation that you need.

this would map to DwC identificationVerificationStatus and
identificationRemarks respectively, right?

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backwards

Certainly somewhere we've been before.

method

That's just labels - we can go there without getting stuck here.

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mkoo on 7 Oct 2019

ID confidence is the new nature of id

But it's not! One can be confident (or not) of IDs of any nature.

identificationVerificationStatus

That's basically a term for a simpler model. We "verify" by adding identifications. I suppose I could somehow stuff something that means "28 people agree on this" (http://arctos.database.museum/guid/MSB:Mamm:55245) in there, but that's not very meaningful without https://github.com/ArctosDB/arctos/issues/2267 - spelling something the same way doesn't necessarily mean you think it's the same thing, and vice-versa.

dustymc on 7 Oct 2019

I like Derek's suggestion of ID confidence + ID method. For method, we want to know if you looked at features first, then based subspecies on geographic distribution, then sequenced and found it's really some other taxon, etc. For observations, maybe it's based on features (saw a moose) or audio-visual.

Add confidence on top of that.

What about adding a third field for ID determination:
field
museum
lab

ccicero on 8 Oct 2019

method

I think that's usefully in id_sensu (which might need a new name? We should get taxon concepts settled in first) - I think every method worth recording is going to require a publication to describe.

I'm not seeing what value
field
museum
lab
would add??

you looked at features first, then based subspecies on geographic distribution, then sequenced

Those should be three IDs.

dustymc on 8 Oct 2019

When will the "legacy" options stop showing up in the data entry screen pick list?

Jegelewicz on 9 Oct 2019

When I get a migration path and they're no longer used.

dustymc on 9 Oct 2019

Yes, those would be three IDs. But I think it's useful to know whether the ID was made in the field (first attempt, without comparative material or more fine-scaled methods) or not. Maybe just a flag "Is this a field ID" ?

I feel like we need to 'regroup.' From what I can tell, here is the latest version (see google doc):

-- fine features + coarse features ---> _I suggest combining these two into a single term 'features', but this is still being debated_
-- function
-- molecular
-- distribution (do we need 'geographic'?)
-- karyotype
-- relationship
-- audio-visual
-- taxonomic revision
-- unknown

Are we agreed on all of these except for whether to break up 'features' ?

Confidence level added to this:
-- unknown (= default?)
-- low
-- medium
-- high

Is this where we stand now?

ccicero on 9 Oct 2019

"Is this a field ID"

I think that takes up back to where we are - random data that doesn't really do anything - but with a lot more work.

without comparative material
fine-scaled methods

I think the idea that those don't exist in the field is a bit discipline-specific. In any case they may have a place here, but they should be quantified/categorized as what they are, not lumped into whatever "field" might mean.

I don't think we have to agree on 'features' except we should get rid of anything that won't be used. (And I believe that ship sailed a few days ago.)

The default for confidence will be NULL. I'm still pretty baffled as to what purpose "unknown" serves or why it is necessary.

Here's current data and proposed mappings.

UAM@ARCTOS> select nature_of_id,count(*) from identification group by nature_of_id order by nature_of_id;

NATURE_OF_ID COUNT(*)

ID of kin 29755 --------------------------> relationship
ID to species group 9591------------------> unknown
coarse features 55------------------------> none/happy
curatorial 14226----------------------> unknown (or features?)
erroneous citation 156------------------------> unknown
expert 725767----------------------> unknown (or features?)
features 269----------------------------->none/happy
field 352627-----------------------> unknown (or features?)
fine features 75-------------------------->none/happy
geographic distribution 25559------------------->none/happy
molecular 13888------------------------->none/happy
photograph 495-----------------------> unknown (or features?)
published referral 3953-----------------------> unknown
revised taxonomy 258734----------------------->none/happy
student 354338-----------------------> unknown (or features?)
type specimen 23663-----------------------> unknown
unknown 2555259-----------------------> >none/happy

Again, PLEASE give me better mapping, globally or for your collection/parts of your collection.

dustymc on 9 Oct 2019

My suggestions in bold (at least for MVZ Birds, and probably for the other MVZ collections although other staff curators should weigh in @atrox10 @mkoo). I still don't like having three terms for 'features' but I guess that's a curatorial call on how we use it.

ID of kin 29755 --------------------------> relationship
ID to species group 9591------------------> unknown CC: features
coarse features 55------------------------> none/happy
curatorial 14226----------------------> unknown (or features?) CC: features
erroneous citation 156------------------------> unknown
expert 725767----------------------> unknown (or features?) CC: features
features 269----------------------------->none/happy
field 352627-----------------------> unknown (or features?) CC: features
fine features 75-------------------------->none/happy
geographic distribution 25559------------------->none/happy
molecular 13888------------------------->none/happy
photograph 495-----------------------> unknown (or features?) CC: features
published referral 3953-----------------------> unknown
revised taxonomy 258734----------------------->none/happy
student 354338-----------------------> unknown (or features?) CC: features
type specimen 23663-----------------------> unknown CC: features
unknown 2555259-----------------------> >none/happy

ccicero on 9 Oct 2019

I agree with Carla's mapping. I also support just using "features" as a
single term.
Do we have a map already from these terms to confidence level?

On Wed, Oct 9, 2019 at 8:59 AM Carla Cicero notifications@github.com
wrote:

My suggestions in bold (at least for MVZ Birds, and probably for the other
MVZ collections although other staff curators should weigh in @atrox10
https://github.com/atrox10 @mkoo https://github.com/mkoo). I still
don't like having three terms for 'features' but I guess that's a
curatorial call on how we use it.

ID of kin 29755 --------------------------> relationship
ID to species group 9591------------------> unknown CC: features
coarse features 55------------------------> none/happy
curatorial 14226----------------------> unknown (or features?) CC:
features
erroneous citation 156------------------------> unknown
expert 725767----------------------> unknown (or features?) CC: features
features 269----------------------------->none/happy
field 352627-----------------------> unknown (or features?) CC: features
fine features 75-------------------------->none/happy
geographic distribution 25559------------------->none/happy
molecular 13888------------------------->none/happy
photograph 495-----------------------> unknown (or features?) CC:
features
published referral 3953-----------------------> unknown
revised taxonomy 258734----------------------->none/happy
student 354338-----------------------> unknown (or features?) CC:
features
type specimen 23663-----------------------> unknown CC: features
unknown 2555259-----------------------> >none/happy

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campmlc on 9 Oct 2019

map already from these terms to confidence level

No - I can handle that if you want, but without feedback from you I think I can only map to NULL.

@DerekSikes has that mapped for his collections in https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537634372 - I can extend that to the default if you'd like.

Do we also need a "taxon description" or something confidence value for the types?

The data suggest that value is not being used correctly which makes me a bit hesitant to double down on it, but it's just a vocabulary term at this point.

  type_status,
  count(*)
from
  identification
  left outer join citation on identification.collection_object_id=citation.collection_object_id
where
  nature_of_id='type specimen'
group by
  type_status
order by
  type_status
 13  ;

TYPE_STATUS          COUNT(*)
------------------------------ ----------
basis of illustration             138
erroneous citation             75
holotype                 1667
host voucher                  598
isolectotype                8
isoneotype              2
isosyntype              4
isotype                   100
lectotype                  48
neotype                 7
paralectotype                  34
paratopotype                 1887
paratype                 3694
referral                  239
symbiotype                162
syntype                    72
voucher                 21049
                     2744

dustymc on 9 Oct 2019

Agree with using Derek's as default with the following additions - please review

ID of kin 29755 --------------------------> relationship confidence high
ID to species group 9591------------------> unknown CC: features confidence low
coarse features 55------------------------> none/happy
curatorial 14226----------------------> unknown (or features?) CC: features confidence high
erroneous citation 156------------------------> unknown confidence low
expert 725767----------------------> unknown (or features?) CC: features confidence high
features 269----------------------------->none/happy
field 352627-----------------------> unknown (or features?) CC: features confidence low
fine features 75-------------------------->none/happy
geographic distribution 25559------------------->none/happy confidence medium
molecular 13888------------------------->none/happy confidence high
photograph 495-----------------------> unknown (or features?) CC: features confidence medium
published referral 3953-----------------------> unknown confidence high
revised taxonomy 258734----------------------->none/happy confidence high
student 354338-----------------------> unknown (or features?) CC: features confidence medium
type specimen 23663-----------------------> unknown CC: features confidence high
unknown 2555259-----------------------> >none/happy

campmlc on 9 Oct 2019

I am happy to map whatever you want for your collection, but as global defaults I have some concerns.

ID of kin 29755 --------------------------> relationship confidence high

This seems wrong to me - the confidence comes from the identification of the related specimen.

ID to species group 9591------------------> unknown CC: features confidence low

I've never been sure of the intent here, but I _think_ it would be "we're fairly confident, but to an imprecise taxon." I have no better suggestions....

erroneous citation 156------------------------> unknown confidence low
That one's just weird - "we're sure we're wrong"???

field 352627-----------------------> unknown (or features?) CC: features confidence low

This is somewhat taxon-dependent, which I probably can't get at for the purposes of migration. This seems correct for shrews, maybe not so much for bison.

revised taxonomy 258734----------------------->none/happy confidence high

I think this also depends on previous IDs. I see no reason "Clethrionomys, maybe" should become "Myodes, definitely."

dustymc on 9 Oct 2019

We use ID of kin for Mexican wolves in an endangered species recovery program. Our confidence in the ID is extremely high. I would hope that they aren't accidentally breeding and releasing coyotes . . .

I could go with ID to species group as medium. You know at least genus.

I don't know about erroneous citation - who uses that? It is in the type definition field.

Agree with revised taxonomy depending on previous, but what about legacy? maybe default to medium?
@DerekSikes @jldunnum

campmlc on 9 Oct 2019

One thing on the "ID of kin" values - for a long time, this was (still is?) the default value in data entry rather than leaving the default as NULL.. Can you send a list of ID of kin specimens so we can verify this is really the case? At MSB, my guess is ID of kin should only legitimately be used for Canis lupus baileyi and possibly embryos cataloged separately.
@jldunnum

campmlc on 9 Oct 2019

erroneous citation - who uses that

https://github.com/ArctosDB/arctos/issues/2170#issuecomment-538076627 or...

guid_prefix, count(*) c 
from collection,cataloged_item,identification where 
  4  nature_of_id='erroneous citation' and collection.collection_id=cataloged_item.collection_id and cataloged_item.collection_object_id=identification.collection_object_id group by guid_prefix order by guid_prefix;

GUID_PREFIX                               C
------------------------------------------------------------ ----------
DGR:Bird                                  1
DMNS:Bird                                15
DMNS:Inv                                  2
KNWR:Ento                                 1
KWP:Ento                                  2
MSB:Mamm                                 45
MVZ:Herp                                  5
MVZ:Mamm                                  1
UAM:ES                                    1
UAM:Ento                                 45
UAM:Herb                                 10
UAM:Mamm                                  1
UAMObs:Ento                              22
UCM:Bird                                  1
UTEP:ES                                   3
UTEP:Herb                                 1

16 rows selected.

what about legacy

Sounds like NULL to me; there's no reason to assert anything you can't know.

list

create table temp_nok as select guid, identification.scientific_name,accepted_id_fg from flat,identification where flat.collection_object_id=identification.collection_object_id and identification.nature_of_id='ID of kin';

temp_nok.csv.zip

dustymc on 9 Oct 2019

Going back to @ ccicero

Yes, those would be three IDs. But I think it's useful to know whether the ID was made in the field (first attempt, without comparative material or more fine-scaled methods) or not. Maybe just a flag "Is this a field ID" ?

What about all of the specimens that are IDed in the lab first rather then the field? I make a lot of quick ID calls when specimens are donated as salvage to the museum, and then stuff them in a freezer for future prepping. I'd count those as Field IDs (just not made in the field), but would this be confusing to someone trying to follow?

ewommack on 10 Oct 2019

Good point Beth. We also use(d) 'field' ID for salvaged specimens prepped in the lab because that was the most fitting option, but it was always strange to do so. I think 'features' takes care of both field and lab preps.

Re: confidence levels mappings:

ID of kin 29755 --------------------------> relationship confidence high
---> I think high is appropriate here, contrary to Dusty's comment. If you know that the parent or sibling is species X, then you should be confident that what you are ID'ing is also species X.

ID to species group 9591------------------> unknown CC: features confidence low

---> I agree with Dusty's comment here. "Medium" seems ok to me.

coarse features 55------------------------> none/happy
curatorial 14226----------------------> unknown (or features?) CC: features confidence high

----> not sure what 'curatorial' means, but I think this would depend on who's doing the ID. If it's a student, then confidence is lower than if ID is by a curator. I'm not sure that we've used this for MVZ collections, can you tell me if we have any with this ID, and the identifier?

erroneous citation 156------------------------> unknown confidence low
expert 725767----------------------> unknown (or features?) CC: features confidence high
features 269----------------------------->none/happy
field 352627-----------------------> unknown (or features?) CC: features confidence low

---> Yes, per Dusty's comment that it would be taxon-dependent. But presumably if you only can ID to a genus in the field, then that's the ID that would have been entered. Or if you're not sure of the ID, then you'd add a "?". So can we get at this through taxa_formula?
if formula contains 'sp' or 'ssp' or 'string' or '?' of 'cf' or 'aff'-or 'A or B' --> confidence is low
if formula contains 'A' or 'A and B' ---> confidence is high
if formula contains 'A / B intergrade' or 'A x B' ---> confidence is low?

fine features 75-------------------------->none/happy
geographic distribution 25559------------------->none/happy confidence medium

---> This can be low or high depending on the taxon and locality, so I am ok with medium.

molecular 13888------------------------->none/happy confidence high
photograph 495-----------------------> unknown (or features?) CC: features confidence medium
published referral 3953-----------------------> unknown confidence high
revised taxonomy 258734----------------------->none/happy confidence high
student 354338-----------------------> unknown (or features?) CC: features confidence medium

---> This can be low or medium depending on the student. We don't use this at MVZ, but I guess medium is ok?

type specimen 23663-----------------------> unknown CC: features confidence high
unknown 2555259-----------------------> >none/happy

ccicero on 10 Oct 2019

@ccicero thanks!

I think there's a bunch of stuff confounded at the intersection of nature and formula. There are ~2500 expert+"A ?" IDs, for example, I'm not sure if that's what you mapped or not. Data attached. I very tentatively suggest we don't pursue that as globals - it's fine for MVZ if that's how it's been used there.

create table temp_lcidf as 
  select 
  guid_prefix, 
  taxa_formula,
  nature_of_id,
  count(*) c 
from 
  collection,
  cataloged_item,
  identification 
where 
 collection.collection_id=cataloged_item.collection_id and 
 cataloged_item.collection_object_id=identification.collection_object_id and
 taxa_formula in ('A ?','A sp.','A ssp.','A {string}','A aff.','A cf.','A or B')
group by 
  guid_prefix, 
  taxa_formula,
  nature_of_id
order by 
  guid_prefix, 
  taxa_formula,
  nature_of_id
;

temp_lcidf.csv.zip

There are a few MVZ/student IDs.

MVZ:Bird 2
MVZ:Herp 18
MVZ:Mamm 858

add a "?"

Good point- can we (long after the dust has settled here!) get rid of that formula, or is it somehow different than confidence?

'A or B'

At least some of those are low-precision but not necessarily low-confidence. "It's one of these two almost-identical shrews; I can't tell them apart." I don't think there's any confidence embedded in that. @amgunderson @KyndallH

dustymc on 10 Oct 2019

add a "?"

Good point- can we (long after the dust has settled here!) get rid of that
formula, or is it somehow different than confidence?

I've long thought that there's serious redundancy between an ID with nature
of ID = student and formula = A ?

One pro of keeping A ? is that string gets sent to GBIF etc and is more
visible than the nature of ID information (I'm not even sure that gets
shared - does it?)

But with ID confidence as a field, it seems silly to retain formula A ?
since this would be the same as confidence = low (or possibly medium).

-Derek

On Thu, Oct 10, 2019 at 8:34 AM dustymc notifications@github.com wrote:

@ccicero https://github.com/ccicero thanks!

I think there's a bunch of stuff confounded at the intersection of nature
and formula. There are ~2500 expert+"A ?" IDs, for example, I'm not sure if
that's what you mapped or not. Data attached. I very tentatively suggest we
don't pursue that as globals - it's fine for MVZ if that's how it's been
used there.

create table temp_lcidf as
select
guid_prefix,
taxa_formula,
nature_of_id,
count(*) c
from
collection,
cataloged_item,
identification
where
collection.collection_id=cataloged_item.collection_id and
cataloged_item.collection_object_id=identification.collection_object_id and
taxa_formula in ('A ?','A sp.','A ssp.','A {string}','A aff.','A cf.','A or B')
group by
guid_prefix,
taxa_formula,
nature_of_id
order by
guid_prefix,
taxa_formula,
nature_of_id
;

temp_lcidf.csv.zip
https://github.com/ArctosDB/arctos/files/3713618/temp_lcidf.csv.zip

There are a few MVZ/student IDs.

MVZ:Bird 2
MVZ:Herp 18
MVZ:Mamm 858

add a "?"

Good point- can we (long after the dust has settled here!) get rid of that
formula, or is it somehow different than confidence?

'A or B'

At least some of those are low-precision but not necessarily
low-confidence. "It's one of these two almost-identical shrews; I can't
tell them apart." I don't think there's any confidence embedded in that.
@amgunderson https://github.com/amgunderson @KyndallH
https://github.com/KyndallH

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+++++++++++++++++++++++++++++++++++
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University of Alaska Museum
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FAX: 907-474-5469

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DerekSikes on 10 Oct 2019

Yes, there is some redundancy between ID with "?" and confidence=low, but I favor keeping the "?" because that is passed to data aggregators whereas confidence is/will not. Also, it makes it evident right in the name that the ID is questionable. I'm not sure how confidence will be displayed, but presumably smaller font below the name?

expert + A ? No, I didn't map that specifically, but that implies (to me) that someone who knows something (e..g. a Jim Patton or Peter Pyle, I would call them both experts) still have some questions about ID. So I don't think we can go strictly from nature of ID to the mapping without considering the formula. In fact, I would say that formula might be more informative for mapping than nature, but for some both need to be considered.

I agree re: 'A or B'.

How's this:

if formula contains 'sp' or 'ssp' or 'string' or '?' of 'cf' or 'aff' --> confidence is low
if formula contains 'A or B' ---> confidence is medium
if formula contains 'A' or 'A and B' ---> use suggested 'nature' mappings
if formula contains 'A / B intergrade' or 'A x B' ---> depends on 'nature' - if molecular, probably higher than by features (?)

Can we get this into a google doc somehow (we already have two going, but it might help to start a clean sheet with these different possible combinations to help in mapping)?

ccicero on 10 Oct 2019

passed to data aggregators

I don't think that's ever a reason to model data - we can map WHATEVER.

not sure how confidence will be displayed

That's UI and "easy" (ish...) to change - you can search now.

Screen Shot 2019-10-10 at 1 11 40 PM

Screen Shot 2019-10-10 at 1 12 22 PM

google doc

Good idea - I'm on it.

dustymc on 10 Oct 2019

This is making my life difficult - I am not able to load anything in the bulkloader because "Legacy nature_of_id terms are disallowed" and I have no idea what to enter in nature of ID anymore....

Jegelewicz on 10 Oct 2019

bulkloader

Let me know if you want me to update something there.

what to enter

http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID

dustymc on 10 Oct 2019

There's the start of a migration document here:

https://docs.google.com/spreadsheets/d/14IOPiv2vHbZv30N3975Y80wf2-_1__Xy1I7ZfXI1FSM/edit?usp=sharing

Please start your review of this in the "first_update" tab. I will make two layers of updates from this if necessary:

I can make smaller-scale updates for specific groups of specimens (collection, institution, whatever). For example, I've mapped that I'll first update all nature_of_id="original_data" to nature_of_id="example" with a confidence of "example" for collection "Fake:Example."
Anything not covered in (1) will be updated for all remaining collections. "type specimen" will become "features" with confidence "high" for any collections that are still using "type specimen" (eg, those that haven't requested a custom update) when I get to this step, for example.

Second, I will update again for everything in the "second_update" tab. So all MVZ specimens with a "A sp." formula are currently mapped to confidence=low, even if they were mapped as confidence=high in the "first_update" tab. If there's agreement on confidence mapping "for_collections" can just be changed to 'all' or similar, if not I will run that step only for those collections that request it.

The existing/old values will still be copied to remarks.

dustymc on 10 Oct 2019

Mapping to aggregators: I agree that we should do what's best for us, but it doesn't hurt to keep the "?" and if we get rid of that and only have confidence, that will likely be buried in a remark somewhere. Given that a lot of requests come through VerNet/GBIF, searches, I think it's worth keeping the "?"

Google doc: I'll look at that as soon as possible, it may be a few days. Thanks.

ccicero on 11 Oct 2019

Sorry I haven't been able to make recent AWG meetings and actually contribute constructively. Instead I'm just sending whiny emails.
A few things:
I know we have lots of IDs which have incorrect nature of ID values generated by our previous DGR collection manager prior to Mariel taking the position. These are primarily the result of inattention to "ID of kin" being set as default or incorrect use of "Type specimen". These remain because we haven't had time to carefully go through them all yet and it is super labor intensive to change them. But I guess this needs to happen quickly now to avoid them being modified and thus harder to track down going forward.

Secondly, I have to say I liked "curatorial" and "field" as they quickly informed that a specimen had either only gone through a provisional first pass in the field or if it had been revisited and examined more closely. I liked being able to see that history and when coupled with ID agent it provided the ID confidence. Now the ID history will appear as "feature" and if looked at again it will have a second "feature", but presumably with a higher confidence value. How will confidence value be displayed? Will it be in the ID history as well?

Overall, I am just very leery about the subjective nature of assigning confidence values (I certainly don't want to assign values to all the legacy IDs which we have no idea on). Even something like "molecular" isn't always going to be high confidence. Just depends on what taxa you included in your analyses or what sequences are available in Genbank when you blasted your sequence.

Jonathan L. Dunnum Ph.D.
Senior Collection Manager
Division of Mammals, Museum of Southwestern Biology
University of New Mexico
Albuquerque, NM 87131
(505) 277-9262
Fax (505) 277-1351

MSB Mammals website: http://www.msb.unm.edu/mammals/index.html
Facebook: http://www.facebook.com/MSBDivisionofMammals

Shipping Address:
Museum of Southwestern Biology
Division of Mammals
University of New Mexico
CERIA Bldg 83, Room 204
Albuquerque, NM 87131

From: dustymc notifications@github.com
Sent: Thursday, October 10, 2019 3:03 PM
To: ArctosDB/arctos arctos@noreply.github.com
Cc: Jonathan Dunnum jldunnum@unm.edu; Mention mention@noreply.github.com
Subject: Re: [ArctosDB/arctos] nature of ID (#2170)

There's the start of a migration document here:

https://docs.google.com/spreadsheets/d/14IOPiv2vHbZv30N3975Y80wf2-_1__Xy1I7ZfXI1FSM/edit?usp=sharing

Please start your review of this in the "first_update" tab. I will make two layers of updates from this if necessary:

I can make smaller-scale updates for specific groups of specimens (collection, institution, whatever). For example, I've mapped that I'll first update all nature_of_id="original_data" to nature_of_id="example" with a confidence of "example" for collection "Fake:Example."
Anything not covered in (1) will be updated for all remaining collections. "type specimen" will become "features" with confidence "high" for any collections that are still using "type specimen" (eg, those that haven't requested a custom update) when I get to this step, for example.

Second, I will update again for everything in the "second_update" tab. So all MVZ specimens with a "A sp." formula are currently mapped to confidence=low, even if they were mapped as confidence=high in the "first_update" tab. If there's agreement on confidence mapping "for_collections" can just be changed to 'all' or similar, if not I will run that step only for those collections that request it.

The existing/old values will still be copied to remarks.

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jldunnum on 11 Oct 2019

labor intensive

As always, I'm happy to try to help that - I just need some way to find existing things and new values. (Sorry I can't help much with the values!)

track down

It's not ideal, but I will retain the old values in remarks, and I can help you find records etc as necessary.

displayed

See https://github.com/ArctosDB/arctos/issues/2170#issuecomment-540767900

history

Yes, it's part of the ID and will be preserved as such.

leery about the subjective nature of assigning confidence values

Yes, I agree, which is why I initially mapped the default to not bring them in at all. It does seem somehow vaguely useful in distinguishing between eg, curatorial and field (which I'd also classify as "vaguely useful" so I don't think much changes there). It also seems very useful to me in noting specific events on specific specimens - "I'm an expert, this is my taxon, I'm not sure about this particular ID because the diagnostic features are mangled" becomes readily searchable rather than something that would have to be extracted from remarks.

In any case I'm happy to do something special for MSB, revise the defaults for everyone, revisit this later from the "old" nature data preserved in remarks, etc.

dustymc on 11 Oct 2019

OK, I'll think about how best to search for our problem children and get back with you with potential ideas. Thanks!

Jonathan L. Dunnum Ph.D.
Senior Collection Manager
Division of Mammals, Museum of Southwestern Biology
University of New Mexico
Albuquerque, NM 87131
(505) 277-9262
Fax (505) 277-1351

MSB Mammals website: http://www.msb.unm.edu/mammals/index.html
Facebook: http://www.facebook.com/MSBDivisionofMammals

Shipping Address:
Museum of Southwestern Biology
Division of Mammals
University of New Mexico
CERIA Bldg 83, Room 204
Albuquerque, NM 87131

From: dustymc notifications@github.com
Sent: Friday, October 11, 2019 11:42 AM
To: ArctosDB/arctos arctos@noreply.github.com
Cc: Jonathan Dunnum jldunnum@unm.edu; Mention mention@noreply.github.com
Subject: Re: [ArctosDB/arctos] nature of ID (#2170)

labor intensive

As always, I'm happy to try to help that - I just need some way to find existing things and new values. (Sorry I can't help much with the values!)

track down

It's not ideal, but I will retain the old values in remarks, and I can help you find records etc as necessary.

displayed

See #2170 (comment)https://github.com/ArctosDB/arctos/issues/2170#issuecomment-540767900

history

Yes, it's part of the ID and will be preserved as such.

leery about the subjective nature of assigning confidence values

Yes, I agree, which is why I initially mapped the default to not bring them in at all. It does seem somehow vaguely useful in distinguishing between eg, curatorial and field (which I'd also classify as "vaguely useful" so I don't think much changes there). It also seems very useful to me in noting specific events on specific specimens - "I'm an expert, this is my taxon, I'm not sure about this particular ID because the diagnostic features are mangled" becomes readily searchable rather than something that would have to be extracted from remarks.

In any case I'm happy to do something special for MSB, revise the defaults for everyone, revisit this later from the "old" nature data preserved in remarks, etc.

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jldunnum on 11 Oct 2019

I just thought about another complication with relates to another issue of multiple IDs in data entry.

If you use can only identify a specimen to genus, and use taxon A, then confidence = high
Same scenario but you use A sp, then confidence = low

Similarly, we often identify a specimen to species (formula A) in the field or during preparation, but then identify it to subspecies in the museum based on either features or distribution. Sometimes we can't ID to subspecies, so we use A ssp. We could leave it as taxon A, but assigning 'ssp' suggests that we tried to ID to subspecies but couldn't with confidence so we didn't. In this scenario:
taxon A = confidence high
taxon A ssp. = confidence low

So it seems to me that you can assign different confidence levels depending on the taxon formula you use.

One way to deal with that, which is what the other issue is getting at, is to allow 2 IDs in data entry/bulkloading. Alternatively, we could do the initial ID in data entry/bulkloading and then go add the second ID/formula once the data are loaded, but that is an extra step and I think it's better to do it at the time you're doing the data entry (especially since there is often a lag between when data are entered by students and checked/loaded by staff).

For data entry/bulkloading, we need a way to add both IDs with the determiner, date, nature, and confidence level, PLUS indicate which is the accepted ID. Can we address the data entry issue along with this issue?

ccicero on 12 Oct 2019

can only identify a specimen to genus, and use taxon A, then confidence = high

I think these are two very different things. "I'm sure it's that genus" and "I think it's probably that genus" are both common scenarios.

assigning 'ssp' suggests that we tried to ID to subspecies but couldn't with confidence so we didn't

That's not what I'd get from there! (I thought it just meant "there are subspecies for this species.") Again I think confounding any >1 concepts is going to lead to confusion. We now have a way to explicitly record confidence, and trying to derive it from anything else is just going to confuse most users.

In any case I could implement https://github.com/ArctosDB/arctos/issues/727 in ~a week (just needs prioritized, especially in relation to PG and the other "emergency" issues that have come up in the past few days), or we might find a way to implement https://github.com/ArctosDB/arctos/issues/2178 as part of SABI, which has the potential to allow any number of just about anything to be loaded ~simultaneously with the core record.

dustymc on 14 Oct 2019

This tripped me up while loading specimen through the bulkloader (both from single entries in Data Entry and from uploaded .csv). I was using 'expert' and 'field' as nature of ID, but the error reads: b_bulkload: b_bulkload: : ORA-20001: Legacy nature_of_id terms are disallowed; see https://github.com/ArctosDB/arctos/issues/2170ORA-06512: at "UAM.TEMP_TR_ID_BIU", line 4ORA-04088: error during exe {snip...}
Can we remove these outdated nature_of_ID's from the dropdowns? Why are we allowed to select these options if they will just fail the validation?
OR: Can we edit the error message to point to the code table instead of this issue (there's a lot to read here)?

Also, there is no 'confidence' field on the Data Entry page.

acdoll on 14 Oct 2019

remove these outdated nature_of_ID's from the dropdowns

Not while they're still used, and something I thought was fully resolved seems to have started over.

point to the code table

Sure - but I think it's already linked everywhere this can be used??

Data Entry

https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537600903

dustymc on 14 Oct 2019

Thanks (and sorry for the repetition, I was skimming too quickly through this issue).

acdoll on 14 Oct 2019

:wave: @dustymc, finalize this

reminders[bot] on 16 Oct 2019

A sp. and A ssp. are the same concepts - you can identify to some level (genus or species but not to species or subspecies, respectively).

Sure, there can be different scenarios where confidence is high or medium or low at any level (confident of genus but not species, or species but not subspecies). That's my point.

Maybe this is (partly?) resolved by getting rid of 'sp' and 'ssp' (and 'aff' and 'cf' ?) and using A {string} for those IDs per issue 1304. If we do that, you'd select A for the genus or species and assign a confidence value, but then put 'sp' or 'ssp' in the string - no need to assign a confidence level to that. However, that still brings up an issue because the way the form is now, you're assigning confidence to the whole ID "A {string}" when really you want to assign confidence to A. So I'm not sure what confidence to assign for "A {string}" when it's 'sp' or 'ssp'

Let's talk about 727 at the next issues meeting. This is high priority for me, especially with the changes, because it's usually a two-step process for identifying specimens to subspecies which is typical for birds and mammals: field/features ID to species, then geographic distribution (plus features in more complicated cases) to subspecies. It would be nice to be able to create bth IDs when doing data entry, each with their own confidence.

FINALLY - regarding migration: when you do the final migration, can you also update the values for nature_of_ID that are in bulkloader files so those users don't have to worry about changing those manually!?

ccicero on 17 Oct 2019

final migration

Unless something drastic happens, I'll probably aim for Friday - Arctos has been really weird for me lately, hopefully that'll help mitigate any meltdowns (or at least give ya'll an excuse to quit early!). Yes I can get the bulkloader too - or I can do that now?

dustymc on 17 Oct 2019

I would just do the bulkloader at the same time.

Arctos has been very SLOW lately, not sure if that's what you're talking about though.

Thanks.

ccicero on 17 Oct 2019

OK I'll plan on that.

Yes that's what I'm talking about - neither I nor TACC can fully explain it, which is making me more paranoid than usual....

dustymc on 17 Oct 2019

Yes, horribly slow today! I was trying to finish a loan to get to Fedex
before the 7pm deadline, and could not get barcodes to load to parts.

On Wed, Oct 16, 2019 at 5:09 PM dustymc notifications@github.com wrote:

OK I'll plan on that.

Yes that's what I'm talking about - neither I nor TACC can fully explain
it, which is making me more paranoid than usual....

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campmlc on 17 Oct 2019

Back to 'features' - Is there a functional difference between 'coarse features' and 'features' ? I can see keeping 'fine features' as separate (looked under a microscope or whatever), but 'looks like a moose' by its features seems the same as by its coarse features. What do folks think about reducing this to just 'features' and 'fine features' to make the data more consistent in how these are used?

ccicero on 17 Oct 2019

Here's who's using %features%

guid_prefix, nature_of_id,count(*) c 
from collection,cataloged_item,identification where 
nature_of_id like '%features' and 
collection.collection_id=cataloged_item.collection_id and 
cataloged_item.collection_object_id=identification.collection_object_id 
  7  group by guid_prefix,nature_of_id order by guid_prefix,nature_of_id;

GUID_PREFIX      NATURE_OF_ID          C
-------------------- -------------------- ----------
BYU:Herp         coarse features          80
BYU:Herp         features            742
BYU:Herp         fine features       121
CHAS:Teach       coarse features          62
CHAS:Teach       fine features         1
DMNS:Bird        features             16
DMNS:Mamm        coarse features           2
DMNS:Mamm        features              8
DMNS:Mamm        fine features         3
KWP:Ento         fine features       179
MSB:Herp         features              5
MSB:Mamm         coarse features         101
MSB:Mamm         features            261
MSB:Mamm         fine features         1
MVZ:Bird         coarse features           9
MVZ:Bird         features             43
MVZ:Herp         features              1
MVZ:Herp         fine features         4
MVZ:Mamm         features              1
UAM:EH           fine features         3
UAM:Ento         coarse features          98
UAM:Ento         fine features        72
UAMObs:Ento      fine features        10
UCM:Bird         coarse features          11
UCM:Bird         fine features         1
UCM:Herp         fine features         1
UCSC:Bird        features            554
UCSC:Herp        features              1
UMNH:Mamm        features              9
UMNH:Teach       features             64
UNR:Herp         features            268
UNR:Mamm         features              4
UWYMV:Fish       features             18

33 rows selected.

dustymc on 17 Oct 2019

I thought we'd given up on the coarse and fine distinction and were just
going with features, which is what I've been using last couple of days.

On Thu, Oct 17, 2019 at 11:22 AM Carla Cicero notifications@github.com
wrote:

Back to 'features' - Is there a functional difference between 'coarse
features' and 'features' ? I can see keeping 'fine features' as separate
(looked under a microscope or whatever), but 'looks like a moose' by its
features seems the same as by its coarse features. What do folks think
about reducing this to just 'features' and 'fine features' to make the data
more consistent in how these are used?

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campmlc on 17 Oct 2019

Is this for new data or per migration requests?

Mariel - That was discussed and what I favored, but I think others still wanted to have more than just 'features.' Like I said, 'fine features' makes some sense. I also am just using 'features' and still think it's worth asking the question about coarse features. What is the functional difference between that and just 'features'?

Dusty - Please change the 9 MVZ:Bird records to just 'features' - Not sure if those are new records, but if they are, then it emphasizes my point about inconsistency in how the data are entered.

ccicero on 17 Oct 2019

Dusty - You're still planning on doing the changes tomorrow, right? Chris says that Jim P is anxious to get his records out of the bulkloader so he can curate specimens from his most recent trip. Thanks.

ccicero on 17 Oct 2019

I'm fine with just 2: 'features' and 'fine features' but the definition for
'features' should mention that this is used for cases when it was unknown
if the examination was of coarse or fine features.. not just an assumption
that the features were not fine.

fine,
D

On Thu, Oct 17, 2019 at 9:42 AM Carla Cicero notifications@github.com
wrote:

Dusty - You're still planning on doing the changes tomorrow, right? Chris
says that Jim P is anxious to get his records out of the bulkloader so he
can curate specimens from his most recent trip. Thanks.

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

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DerekSikes on 17 Oct 2019

change the 9 MVZ:Bird

done

changes tomorrow,

If I think I can without melting something important, yes.

out of the bulkloader

I can help with that at any time, or that should be straightforward with SQL option.

dustymc on 17 Oct 2019

Thanks Derek. I agree re: definition.

Dusty - Can you go ahead and make the nature of ID change to the records under username 'patton' in the bulklloader? Then he can load them. Thanks.

ccicero on 17 Oct 2019

patton

Done

dustymc on 17 Oct 2019

We're getting error messages when we try to update an identification on an existing record. The messages refer us to this Issue but I don't see a resolution here.

This is our first update attempt.

ID error - input

This is the error message which directs us to this issue.

Error message

The handbook references #515.

We are not trying to use "legacy" as the initial ID, so is the error message a bug?

If we select "revised taxonomy" for the new ID, we sometimes get this error message. We get whether or not we have completed the "confidence" field.

revised taxonomy

Right now, we seem locked out of updating identifications.

sharpphyl on 17 Oct 2019

P.S. We can get it to work with some other selections such as "audio-visual" then change it to student or revised taxonomy before we save it.

sharpphyl on 17 Oct 2019

Thanks D.

Phyllis - 'student' is a legacy value that's no longer allowed. As soon as Dusty makes the changes (hopefully tomorrow), he'll clean up the list so it only has the new values. Sorry for the inconvenience in the interim.

ccicero on 17 Oct 2019

Thanks, Carla. I can't find in this thread what "student" will be changed to (like "legacy" was changed to "unknown"). Is the new value in the list? Or is it just a confidence level? Sorry I didn't keep up with this thread.

sharpphyl on 17 Oct 2019

See http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID for terminology and https://docs.google.com/spreadsheets/d/14IOPiv2vHbZv30N3975Y80wf2-_1__Xy1I7ZfXI1FSM/edit#gid=1160354566 for the "unless someone tells me otherwise..." mapping.

dustymc on 17 Oct 2019

OK, so "student" will become "features" at medium confidence. Thanks.

sharpphyl on 17 Oct 2019

For the terminology:

audio-visual

might be better as

audio-video

which would unambiguously match its definition. Currently I could see
someone unfamiliar with the definitions using this as a synonym of
features. Changing visual to video would prevent that.

And I think we agreed to eliminate 'coarse features' and just use 'features'

And I will reiterate that 'type specimen' should not become legacy - there
are lots of such IDs that lack citations and eliminating this option would
toss valuable data.

-Derek

On Thu, Oct 17, 2019 at 11:36 AM dustymc notifications@github.com wrote:

See
http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID
for terminology and
https://docs.google.com/spreadsheets/d/14IOPiv2vHbZv30N3975Y80wf2-_1__Xy1I7ZfXI1FSM/edit#gid=1160354566
for the "unless someone tells me otherwise..." mapping.

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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact_us http://www.akentsoc.org/contact.php

DerekSikes on 17 Oct 2019

eliminate 'coarse features'

I'd just need a map for those that have used it - https://github.com/ArctosDB/arctos/issues/2170#issuecomment-543281386

type specimen

PLEASE, suggest a better mapping! https://docs.google.com/spreadsheets/d/14IOPiv2vHbZv30N3975Y80wf2-_1__Xy1I7ZfXI1FSM/edit#gid=1160354566 (And remarks will catch anything that gets tossed.)

dustymc on 17 Oct 2019

The thing about 'type specimen' that is special and worth keeping (no need
to map if it's not changing... or just map to itself) is that when a
taxonomist describes a taxon and designates a type specimen they've often
done a hell of a lot more than what is encompassed in id method =
'features'.

They've compared those specimens to numerous others, assessed variation
across space / populations / close relatives etc. In some cases, they've
used molecular methods to assess genetic uniqueness as well as 'features'
and in other cases, rarely, they might have actually used ecological/
behavioral data to assess species status. They might have even done
breeding trials.

Regardless of how many different methods they've used, even if they
described the new species based only on 'features' there's a huge
difference between using a key someone else wrote to key out an unknown
using 'features' and a taxonomist describing a new species, and WRITING the
key and describing the species.

Additionally, because of the rules of nomenclature, type specimens ALWAYS
belong to the name - even if that name has later been deemed to not
represent a distinct species the type specimen is tied to that name by the
"laws" of nomenclature.

All this cannot be summarized as 'features' and thus I argue that 'type
specimen' should not become legacy but should remain in our list of nature
of ID options.

-Derek

On Thu, Oct 17, 2019 at 12:18 PM dustymc notifications@github.com wrote:

eliminate 'coarse features'

I'd just need a map for those that have used it - #2170 (comment)
https://github.com/ArctosDB/arctos/issues/2170#issuecomment-543281386

type specimen

PLEASE, suggest a better mapping!
https://docs.google.com/spreadsheets/d/14IOPiv2vHbZv30N3975Y80wf2-_1__Xy1I7ZfXI1FSM/edit#gid=1160354566
(And remarks will catch anything that gets tossed.)

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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact_us http://www.akentsoc.org/contact.php

DerekSikes on 17 Oct 2019

I like audio-video

I also agree that 'type specimen' should remain an option in the list.

ccicero on 17 Oct 2019

In some cases, they've
used molecular methods to assess genetic uniqueness as well as 'features'
and in other cases, rarely, they might have actually used ecological/
behavioral data to assess species status. They might have even done
breeding trials.

That is precisely the information I think we need to capture; if you're a whateverologist, you might want to find types defined by somethingelseology (eg, because you want to see if morphology and COI agree, or .....). Tossing all of that into "type specimen" won't support any of those questions.

A search on typestatus like %type (or something more specific) + nature_of_id=features WILL find those specimens.

If there's some value in these data, I suggest we follow MCZ's lead and create a "random types with no more information" publication to make the correct links (eg, make them discoverable along with well-documented types), even if we do it with a low-quality publication. (That probably needs a new "unknown type" or similar status??)

I checked a half-dozen of these, one of them looks like it's probably really an undocumented paratype, the rest I'm fairly certain just have random values here.

Here's a summary:

col guid_prefix format a30;
select guid_prefix, count(*) c from collection,cataloged_item,identification where 
collection.collection_id=cataloged_item.collection_id and
cataloged_item.collection_object_id=identification.collection_object_id
and identification.nature_of_id='type specimen'
and not exists (select collection_object_id from citation where citation.collection_object_id=cataloged_item.collection_object_id and type_status like '%type')
group by guid_prefix order by guid_prefix;


GUID_PREFIX             C
------------------------------ ----------
ALMNH:ES                3
DGR:Bird                6
DGR:Mamm                1
DMNS:Bird               3
DMNS:Mamm                  17
HWML:Para                1710
KNWR:Ento               9
MLZ:Bird                2
MSB:Bird                   10
MSB:Fish                8
MSB:Host                1
MSB:Mamm                 4436
MSB:Para                   44
MVZ:Bird                  130
MVZ:Herp                  518
MVZ:Mamm                 1109
MVZObs:Herp             1
UAM:Bird                  156
UAM:Ento                3
UAM:Fish                2
UAM:Herb                  218
UAM:Herp                2
UAM:Inv                 9
UAM:Mamm                 6699
UAMObs:Ento                53
UAMObs:Mamm             7
UCM:Fish                   21
UCM:Herp                  442
UCM:Mamm                   26
USNPC:Para              1
UTEP:ES                    12
UTEP:Ento                  20
UTEP:Herb                  15
UTEP:Herp                 300
UTEP:HerpOS             1
UTEP:Inv                   20
UTEP:Zoo                   23
UWBM:Herp               2

and data

create table temp_undoctypes as select guid from flat,identification where flat.collection_object_id=identification.collection_object_id
and identification.nature_of_id='type specimen'
and not exists (select collection_object_id from citation where citation.collection_object_id=flat.collection_object_id and type_status like '%type')
order by guid;

temp_undoctypes.csv.zip

dustymc on 17 Oct 2019

It should not be up to the data entry technicians to assess all the methods
that were used by an author who describes a species. All they know is that
it's a type specimen and thus it's important to flag it as such EVEN if the
citation / publication is unknown.

-Derek

On Thu, Oct 17, 2019 at 1:00 PM dustymc notifications@github.com wrote:

In some cases, they've
used molecular methods to assess genetic uniqueness as well as 'features'
and in other cases, rarely, they might have actually used ecological/
behavioral data to assess species status. They might have even done
breeding trials.

That is precisely the information I think we need to capture; if you're a
whateverologist, you might want to find types defined by somethingelseology
(eg, because you want to see if morphology and COI agree, or .....).
Tossing all of that into "type specimen" won't support any of those
questions.

A search on typestatus like %type (or something more specific) +
nature_of_id=features WILL find those specimens.

If there's some value in these data, I suggest we follow MCZ's lead and
create a "random types with no more information" publication to make the
correct links (eg, make them discoverable along with well-documented
types), even if we do it with a low-quality publication. (That probably
needs a new "unknown type" or similar status??)

I checked a half-dozen of these, one of them looks like it's probably
really an undocumented paratype, the rest I'm fairly certain just have
random values here.

Here's a summary:

col guid_prefix format a30;
select guid_prefix, count(*) c from collection,cataloged_item,identification where
collection.collection_id=cataloged_item.collection_id and
cataloged_item.collection_object_id=identification.collection_object_id
and identification.nature_of_id='type specimen'
and not exists (select collection_object_id from citation where citation.collection_object_id=cataloged_item.collection_object_id and type_status like '%type')
group by guid_prefix order by guid_prefix;

GUID_PREFIX C

ALMNH:ES DGR:Bird DGR:Mamm DMNS:Bird DMNS:Mamm HWML:Para KNWR:Ento MLZ:Bird MSB:Bird MSB:Fish MSB:Host MSB:Mamm MSB:Para MVZ:Bird MVZ:Herp MVZ:Mamm MVZObs:Herp UAM:Bird UAM:Ento UAM:Fish UAM:Herb UAM:Herp UAM:Inv UAM:Mamm UAMObs:Ento UAMObs:Mamm UCM:Fish UCM:Herp UCM:Mamm USNPC:Para UTEP:ES UTEP:Ento UTEP:Herb UTEP:Herp UTEP:HerpOS UTEP:Inv UTEP:Zoo UWBM:Herp 3
6
1
3
17
1710
9
2
10
8
1
4436
44
130
518
1109
1
156
3
2
218
2
9
6699
53
7
21
442
26
1
12
20
15
300
1
20
23
2

and data

create table temp_undoctypes as select guid from flat,identification where flat.collection_object_id=identification.collection_object_id
and identification.nature_of_id='type specimen'
and not exists (select collection_object_id from citation where citation.collection_object_id=flat.collection_object_id and type_status like '%type')
order by guid;

temp_undoctypes.csv.zip
https://github.com/ArctosDB/arctos/files/3741268/temp_undoctypes.csv.zip

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Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
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DerekSikes on 18 Oct 2019

important to flag it

How important? What's there (apparently-incorrect data aside) requires some knowledge of an arbitrary administrative process, at least two queries to find all the types, and displaces methodology from "nature." What I laid out works like everything else, doesn't require your techs to assess anything ('unknown' is always an option), doesn't need a specific publication, and there's a place for method-based 'nature' if it is known.

In any case I can drop this out of the migration if that's what's best.

dustymc on 18 Oct 2019

I'd argue that 'type specimen' is a method. It's a method that employs the
rules of nomenclature to assert this specimen is this taxon.

Why would it require 2 queries to find all the types- because some won't
have nature of id = type specimen? I can see that being a problem but it's
easily fixed by setting that field to = type specimen for all type
specimens. However, it'd be hard to enforce consistency though, people
could use the citation / holotype option and for the nature of ID choose
something besides 'type specimen'

You say that what you laid out "doesn't need a specific publication" - how
then can one specify a specimen is a type without creating a citation from
a publication?

Another option, and what I've done in databases I've made and used in the
past, is to have a field dedicated to 'type status' and most specimens
would be 'none' but all the type specimens would have something in that
field like 'holotype' etc.

Is there a Darwin core field for that?

-D

On Thu, Oct 17, 2019 at 4:36 PM dustymc notifications@github.com wrote:

important to flag it

How important? What's there (apparently-incorrect data aside) requires
some knowledge of an arbitrary administrative process, at least two queries
to find all the types, and displaces methodology from "nature." What I laid
out works like everything else, doesn't require your techs to assess
anything ('unknown' is always an option), doesn't need a specific
publication, and there's a place for method-based 'nature' if it is known.

In any case I can drop this out of the migration if that's what's best.

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Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
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DerekSikes on 18 Oct 2019

argue that 'type specimen' is a method

I'm not sure that's WRONG, but there's also a lot of noise from folks who might want to find the resulting types when someone magicks a species out of DNA or photos or other nontraditional methods. As far as I know similar data have never been published - who knows, maybe nobody will use it, they definitely won't if we structure our data such that the information isn't accessible.

2 queries

"Real" types in Arctos require publications; that's the way most users will find them, and it's what I use for DWC and reporting and etc. (Yes DWC has a field.)

setting that field to = type specimen for all type specimens

I suppose that's a curatorial call, but it's definitely not something I'd recommend.

how then can one specify a specimen is a type without creating a citation from
a publication?

You can't, but it's easy to materialize publications. https://mczbase.mcz.harvard.edu/SpecimenUsage.cfm?action=search&publication_id=35944 exists to allow "normal" access to types without forcing you to actually track down the real publication. (I think they've got it a little too fine-grained, but the idea seems to work well enough - and the fake publications aren't holding thousands of records that REALLY don't look like types, which is nice!)

field dedicated to 'type status'

Yea, that's the norm. I don't think I've ever got much information out of one. I suppose we could spin up an attribute for that but then users would find it, use it to locate the few percentage of alleged types that aren't supported by publications, and leave thinking they've found what we have.

dustymc on 18 Oct 2019

OK, I'm convinced.

Best to do things only 1 way.

-Derek

On Thu, Oct 17, 2019 at 6:34 PM dustymc notifications@github.com wrote:

argue that 'type specimen' is a method

I'm not sure that's WRONG, but there's also a lot of noise from folks who
might want to find the resulting types when someone magicks a species out
of DNA or photos or other nontraditional methods. As far as I know similar
data have never been published - who knows, maybe nobody will use it, they
definitely won't if we structure our data such that the information isn't
accessible.

2 queries

"Real" types in Arctos require publications; that's the way most users
will find them, and it's what I use for DWC and reporting and etc. (Yes DWC
has a field.)

setting that field to = type specimen for all type specimens

I suppose that's a curatorial call, but it's definitely not something I'd
recommend.

how then can one specify a specimen is a type without creating a citation
from
a publication?

You can't, but it's easy to materialize publications.
https://mczbase.mcz.harvard.edu/SpecimenUsage.cfm?action=search&publication_id=35944
exists to allow "normal" access to types without forcing you to actually
track down the real publication. (I think they've got it a little too
fine-grained, but the idea seems to work well enough - and the fake
publications aren't holding thousands of records that REALLY don't look
like types, which is nice!)

field dedicated to 'type status'

Yea, that's the norm. I don't think I've ever got much information out of
one. I suppose we could spin up an attribute for that but then users would
find it, use it to locate the few percentage of alleged types that aren't
supported by publications, and leave thinking they've found what we have.

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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
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DerekSikes on 18 Oct 2019

🎉1

Sweet!

Lacking better ideas materializing in the very near future, I will

create a new type status "unknown type" (so it'll show up in the "any TYPE" search) definition "DO NOT USE! Placeholder for records which were flagged with identification.nature_of_id type specimen, and which cannot currently be resolved to more specific Types and publications."
create a 'placeholder for type specimens' publication
create a citation using those data for all NoID=type specimen records which do not have an existing %type citation
file a 'please clean this up' issue (I think many/most of these are noise, not actual types)

Reasonable?

dustymc on 18 Oct 2019

I'd like to revise the above.

There are ~16K specimens with a NoID of "type specimen" which do not have a corresponding 'type' type_status, but >10K of them do have a publication (usually citing 'voucher') on the 'type specimen' identification. I think those are clearly just using 'type specimen' (as NoID) in a slightly different way, NOT attempting to use NoID as a placeholder for type specimens. Unless someone has a compelling reason to do otherwise, I will ignore those and only create citations (using the new fake publication) for the ~5K citations which use NoID "type specimen" without a corresponding publication.

dustymc on 18 Oct 2019

Out of curiosity, are there records that have NoID of 'type specimen' and have a type_status other than 'voucher' - i.e., ones that are actual types where it is a placeholder for type specimens?

Can you send me a csv of the 130 MVZ:Bird records that have NoID of 'type specimen' so I can look at those? Thanks.

ccicero on 18 Oct 2019

are there records that have NoID of 'type specimen' and have a type_status other than 'voucher'

col type_status format a20;
select  citation.type_status, count(*)  from 
 flat,identification,citation
 where
 flat.collection_object_id=identification.collection_object_id and
 identification.identification_id=citation.identification_id and
identification.nature_of_id='type specimen' and
citation.type_status!='voucher'
group by citation.type_status
;


TYPE_STATUS        COUNT(*)
-------------------- ----------
holotype            929
isosyntype            2
basis of illustratio        108
n

paratype           2725
erroneous citation       53
isotype              50
isolectotype              4
lectotype            45
symbiotype           78
neotype               3
referral            197
isoneotype            1
paratopotype           1037
syntype              64
host voucher            423
paralectotype            30

placeholder

Those are ACTUAL citations; I'm using the word "placeholder" for things that don't have citations (yet - they'll get them, but against a fake publication) but have some indication that they might be types. (So now the data essentially say "this is a type, here's the publication" and "this is a type, we just say so." This change will provide the possibility to turn the latter into "this is a type, it's based on features, it's a really great candidate for a molecular study!")

csv

It's attached to https://github.com/ArctosDB/arctos/issues/2170#issuecomment-543360029

dustymc on 18 Oct 2019

All catalog records with a 'type specimen' NoID are now attached to a publication; those that weren't already attached to something are on http://arctos.database.museum/publication/10008933

dustymc on 18 Oct 2019

Thanks!

ccicero on 18 Oct 2019

We need the new 'confidence' field in the data entry screen.

-Derek

On Fri, Oct 18, 2019 at 9:47 AM Carla Cicero notifications@github.com
wrote:

Thanks!

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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological
Society and / or sign up for the email listserv "Alaska Entomological
Network" at
http://www.akentsoc.org/contact_us http://www.akentsoc.org/contact.php

DerekSikes on 18 Oct 2019

data entry
https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537600903

dustymc on 18 Oct 2019

Yes I’d like to see the mvz herps like that too

On Fri, Oct 18, 2019 at 9:19 AM Carla Cicero notifications@github.com
wrote:

Out of curiosity, are there records that have NoID of 'type specimen' and
have a type_status other than 'voucher' - i.e., ones that are actual types
where it is a placeholder for type specimens?

Can you send me a csv of the 130 MVZ:Bird records that have NoID of 'type
specimen' so I can look at those? Thanks.

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atrox10 on 18 Oct 2019

I don't know what went on here but you have turned 1 simple and understandable field into a mess. I would like to load records identified by students, I have entered 100s of records with the nature of ID "student" but now I assume it should be "course features" with a confidence level that is pulled out of my a**? Where is the confidence level field in the bulk loader menu? I need to change "student" to "course features" but there is no way to add a confidence level from the bulkload SQL page and it doesn't appear at all in the AJAX page.

amgunderson on 19 Oct 2019

Updates including bulkloader are done and the code table is cleaned up. It will take a couple days for everything to find its way to all forms. Closing this monstrosity; I opened a couple new issues for everything, I hope, that still needs handled.

confidence level that is pulled out of my a**?

I'd say that's NULL (='we have nothing informative to say, so we'll say nothing'), and at least earlier in this thread I was under the strong impression that that would be the case most of the time. Please prioritize https://github.com/ArctosDB/arctos/issues/2323 if there is an immediate need to assert confidence in data entry/bulkloaders.

dustymc on 19 Oct 2019

@dustymc
Please edit the Edit Citation/ Create Citation And Identification tool so that the default Nature of ID is NULL. Currently it is set to audio-visual. All dropdowns should always have a null default.

campmlc on 23 Nov 2019

Arctos: nature of ID

All 247 comments

2160

1093https://github.com/ArctosDB/arctos/issues/1093

1093 https://github.com/ArctosDB/arctos/issues/1093

1093 https://github.com/ArctosDB/arctos/issues/1093

>

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